diff --git a/README.md b/README.md
index d52e98b..1f0115b 100644
--- a/README.md
+++ b/README.md
@@ -135,6 +135,13 @@ foreign key relationship is
 which would also be dropped and recreated. Therefore this option is disabled by
 default, and FOREIGN KEY differences will cause the tool to fail.
 
+## Note on Proto Bundles
+
+This tool does not support diffing of `PROTO BUNDLE` statements. By default, the tool will fail if it encounters a `PROTO BUNDLE` statement in the DDL.
+If you are confident that you do not need to diff `PROTO BUNDLE` statements, you can use the `--ignoreProtoBundles` flag. When this flag is set, the tool will ignore any `PROTO BUNDLE` statements in the DDL and will not generate any `ALTER` statements for them.
+
+**Warning:** This is a feature for a specific use case. Only use this flag if you are confident in your knowledge of how it will work.
+
 ## Unsupported Spanner DDL features
 
 This tool by neccessity will lag behind the implementation of new DDL features
@@ -172,6 +179,7 @@ mvn generate-resources compile exec:java \
   -Dexec.args="\
       --allowRecreateIndexes
       --allowRecreateForeignKeys
+      --ignoreProtoBundles
       --originalDdlFile original.ddl
       --newDdlFile new.ddl
       --outputDdlFile alter.ddl
@@ -185,6 +193,7 @@ mvn clean generate-resources compile package
 
 java -jar target/spanner-ddl-diff-*-jar-with-dependencies.jar \
       --allowRecreateIndexes \
+      --ignoreProtoBundles \
       --originalDdlFile original.ddl \
       --newDdlFile new.ddl \
       --outputDdlFile alter.ddl
@@ -334,6 +343,7 @@ generating statements to drop and recreate the constraint.
     --allowRecreateIndexes        Allows dropping and recreating secondary
                                   Indexes to apply changes.
     --help                        Show help.
+    --ignoreProtoBundles          Ignores proto bundle definitions.
     --newDdlFile <FILE>           File path to the new DDL definition.
     --originalDdlFile <FILE>      File path to the original DDL definition.
     --outputDdlFile <FILE>        File path to the output DDL to write.
diff --git a/src/main/java/com/google/cloud/solutions/spannerddl/diff/DatabaseDefinition.java b/src/main/java/com/google/cloud/solutions/spannerddl/diff/DatabaseDefinition.java
index c80fdcd..cd97e55 100644
--- a/src/main/java/com/google/cloud/solutions/spannerddl/diff/DatabaseDefinition.java
+++ b/src/main/java/com/google/cloud/solutions/spannerddl/diff/DatabaseDefinition.java
@@ -35,6 +35,7 @@
 import com.google.common.collect.ImmutableMap;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Optional;
 
 /**
@@ -54,7 +55,8 @@ public abstract class DatabaseDefinition {
    * @param statements List of parsed DDL statements
    * @return DatabaseDefinition instance
    */
-  public static DatabaseDefinition create(List<ASTddl_statement> statements) {
+  public static DatabaseDefinition create(
+      List<ASTddl_statement> statements, Map<String, Boolean> options) {
     // Use LinkedHashMap to preserve creation order in original DDL.
     LinkedHashMap<String, ASTcreate_table_statement> tablesInCreationOrder = new LinkedHashMap<>();
     LinkedHashMap<String, ASTcreate_index_statement> indexes = new LinkedHashMap<>();
@@ -128,6 +130,13 @@ public static DatabaseDefinition create(List<ASTddl_statement> statements) {
               (ASTcreate_change_stream_statement) statement);
           break;
 
+        case DdlParserTreeConstants.JJTCREATE_PROTO_BUNDLE_STATEMENT:
+        case DdlParserTreeConstants.JJTALTER_PROTO_BUNDLE_STATEMENT:
+          if (!options.get(DdlDiff.IGNORE_PROTO_BUNDLES_OPT)) {
+            throw new UnsupportedOperationException("Not Implemented");
+          }
+          break;
+
         case DdlParserTreeConstants.JJTCREATE_OR_REPLACE_STATEMENT:
           // can be one of several types.
           switch (((ASTcreate_or_replace_statement) statement).getSchemaObject().getId()) {
diff --git a/src/main/java/com/google/cloud/solutions/spannerddl/diff/DdlDiff.java b/src/main/java/com/google/cloud/solutions/spannerddl/diff/DdlDiff.java
index ab29370..e1e25c2 100644
--- a/src/main/java/com/google/cloud/solutions/spannerddl/diff/DdlDiff.java
+++ b/src/main/java/com/google/cloud/solutions/spannerddl/diff/DdlDiff.java
@@ -71,14 +71,14 @@
  *
  * <p>Example usage:
  *
- * <p>Pass the original and new DDL text to the {@link #build(String, String)} function, and call
- * {@link #generateDifferenceStatements(Map)} to generate the list of {@code ALTER} statements.
+ * <p>Pass the original and new DDL text to the {@link #build(String, String, Map)} function, and
+ * call {@link #generateDifferenceStatements(Map)} to generate the list of {@code ALTER} statements.
  *
  * <p>eg:
  *
  * <pre>
- * List&lt;String&gt; statements = DdlDiff.build(originalDDL, newDDL)
- *    .generateDifferenceStatements(true, true);
+ * List&lt;String&gt; statements = DdlDiff.build(originalDDL, newDDL,
+ * java.util.Collections.emptyMap()).generateDifferenceStatements(java.util.Collections.emptyMap());
  * </pre>
  *
  * <p>or execute the {@link #main(String[]) main()} function with the {@link
@@ -93,6 +93,7 @@ public class DdlDiff {
   public static final String ALLOW_RECREATE_INDEXES_OPT = "allowRecreateIndexes";
   public static final String ALLOW_RECREATE_CONSTRAINTS_OPT = "allowRecreateConstraints";
   public static final String ALLOW_DROP_STATEMENTS_OPT = "allowDropStatements";
+  public static final String IGNORE_PROTO_BUNDLES_OPT = "ignoreProtoBundles";
   public static final String HELP_OPT = "help";
 
   private final DatabaseDefinition originalDb;
@@ -670,7 +671,8 @@ private static String generateOptionsUpdates(MapDifference<String, String> optio
    * @return DdlDiff instance
    * @throws DdlDiffException if there is an error in paring the DDL
    */
-  public static DdlDiff build(String originalDdl, String newDdl) throws DdlDiffException {
+  public static DdlDiff build(String originalDdl, String newDdl, Map<String, Boolean> options)
+      throws DdlDiffException {
     List<ASTddl_statement> originalStatements;
     List<ASTddl_statement> newStatements;
     try {
@@ -684,8 +686,8 @@ public static DdlDiff build(String originalDdl, String newDdl) throws DdlDiffExc
       throw new DdlDiffException("Failed parsing NEW DDL: " + e.getMessage(), e);
     }
 
-    DatabaseDefinition originalDb = DatabaseDefinition.create(originalStatements);
-    DatabaseDefinition newDb = DatabaseDefinition.create(newStatements);
+    DatabaseDefinition originalDb = DatabaseDefinition.create(originalStatements, options);
+    DatabaseDefinition newDb = DatabaseDefinition.create(newStatements, options);
 
     return new DdlDiff(
         originalDb, newDb, getDatabaseNameFromAlterDatabase(originalStatements, newStatements));
@@ -818,6 +820,8 @@ public static List<ASTddl_statement> parseDdl(String original, boolean parseAnno
           case DdlParserTreeConstants.JJTALTER_DATABASE_STATEMENT:
           case DdlParserTreeConstants.JJTCREATE_CHANGE_STREAM_STATEMENT:
           case DdlParserTreeConstants.JJTCREATE_SEARCH_INDEX_STATEMENT:
+          case DdlParserTreeConstants.JJTCREATE_PROTO_BUNDLE_STATEMENT:
+          case DdlParserTreeConstants.JJTALTER_PROTO_BUNDLE_STATEMENT:
             // no-op - allowed
             break;
           case DdlParserTreeConstants.JJTCREATE_OR_REPLACE_STATEMENT:
@@ -860,9 +864,9 @@ public static void main(String[] args) {
       String originalDdl = new String(Files.readAllBytes(options.originalDdlPath()), UTF_8);
       String newDdl = new String(Files.readAllBytes(options.newDdlPath()), UTF_8);
 
-      validateDdl(newDdl);
+      validateDdl(newDdl, options.args());
 
-      DdlDiff ddlDiff = DdlDiff.build(originalDdl, newDdl);
+      DdlDiff ddlDiff = DdlDiff.build(originalDdl, newDdl, options.args());
 
       List<String> alterStatements = ddlDiff.generateDifferenceStatements(options.args());
 
@@ -890,14 +894,14 @@ public static void main(String[] args) {
    * @param ddl new DDL to parse
    * @throws DdlDiffException if there is an error in parsing the DDL
    */
-  public static void validateDdl(String ddl) throws DdlDiffException {
+  public static void validateDdl(String ddl, Map<String, Boolean> options) throws DdlDiffException {
     List<ASTddl_statement> statements;
     try {
       statements = parseDdl(Strings.nullToEmpty(ddl));
     } catch (DdlDiffException e) {
       throw new DdlDiffException("Failed parsing DDL: " + e.getMessage(), e);
     }
-    DatabaseDefinition db = DatabaseDefinition.create(statements);
+    DatabaseDefinition db = DatabaseDefinition.create(statements, options);
     validateReferences(db);
   }
 
diff --git a/src/main/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffOptions.java b/src/main/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffOptions.java
index b6aa8a4..8eb570a 100644
--- a/src/main/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffOptions.java
+++ b/src/main/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffOptions.java
@@ -92,6 +92,11 @@ static Options buildOptions() {
             .longOpt(DdlDiff.ALLOW_DROP_STATEMENTS_OPT)
             .desc("Enables output of DROP commands to delete objects not used in the new DDL file.")
             .build());
+    options.addOption(
+        Option.builder()
+            .longOpt(DdlDiff.IGNORE_PROTO_BUNDLES_OPT)
+            .desc("Ignores proto bundle definitions when parsing DDLs and generating diffs.")
+            .build());
     options.addOption(Option.builder().longOpt(DdlDiff.HELP_OPT).desc("Show help").build());
     return options;
   }
@@ -155,7 +160,9 @@ public static DdlDiffOptions parseCommandLine(String[] args) {
               DdlDiff.ALLOW_DROP_STATEMENTS_OPT,
                   commandLine.hasOption(DdlDiff.ALLOW_DROP_STATEMENTS_OPT),
               DdlDiff.ALLOW_RECREATE_CONSTRAINTS_OPT,
-                  commandLine.hasOption(DdlDiff.ALLOW_RECREATE_CONSTRAINTS_OPT));
+                  commandLine.hasOption(DdlDiff.ALLOW_RECREATE_CONSTRAINTS_OPT),
+              DdlDiff.IGNORE_PROTO_BUNDLES_OPT,
+                  commandLine.hasOption(DdlDiff.IGNORE_PROTO_BUNDLES_OPT));
 
       return new AutoValue_DdlDiffOptions(originalDdlPath, newDdlPath, outputDdlPath, argsMap);
     } catch (InvalidPathException e) {
diff --git a/src/main/java/com/google/cloud/solutions/spannerddl/parser/ASTalter_proto_bundle_statement.java b/src/main/java/com/google/cloud/solutions/spannerddl/parser/ASTalter_proto_bundle_statement.java
index c03bb34..177fd03 100644
--- a/src/main/java/com/google/cloud/solutions/spannerddl/parser/ASTalter_proto_bundle_statement.java
+++ b/src/main/java/com/google/cloud/solutions/spannerddl/parser/ASTalter_proto_bundle_statement.java
@@ -18,11 +18,9 @@
 public class ASTalter_proto_bundle_statement extends SimpleNode {
   public ASTalter_proto_bundle_statement(int id) {
     super(id);
-    throw new UnsupportedOperationException("Not Implemented");
   }
 
   public ASTalter_proto_bundle_statement(DdlParser p, int id) {
     super(p, id);
-    throw new UnsupportedOperationException("Not Implemented");
   }
 }
diff --git a/src/main/java/com/google/cloud/solutions/spannerddl/parser/ASTcreate_proto_bundle_statement.java b/src/main/java/com/google/cloud/solutions/spannerddl/parser/ASTcreate_proto_bundle_statement.java
index 91da270..6a8cffd 100644
--- a/src/main/java/com/google/cloud/solutions/spannerddl/parser/ASTcreate_proto_bundle_statement.java
+++ b/src/main/java/com/google/cloud/solutions/spannerddl/parser/ASTcreate_proto_bundle_statement.java
@@ -18,11 +18,9 @@
 public class ASTcreate_proto_bundle_statement extends SimpleNode {
   public ASTcreate_proto_bundle_statement(int id) {
     super(id);
-    throw new UnsupportedOperationException("Not Implemented");
   }
 
   public ASTcreate_proto_bundle_statement(DdlParser p, int id) {
     super(p, id);
-    throw new UnsupportedOperationException("Not Implemented");
   }
 }
diff --git a/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffFromFilesTest.java b/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffFromFilesTest.java
index b172c90..a016eb4 100644
--- a/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffFromFilesTest.java
+++ b/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffFromFilesTest.java
@@ -62,7 +62,11 @@ public void compareDddTextFiles() throws IOException {
                 : Collections.emptyList();
 
         LOG.info("Processing segment (with drops): " + segmentName);
-        DdlDiff ddlDiff = DdlDiff.build(originalSegment.getValue(), newSegment.getValue());
+        DdlDiff ddlDiff =
+            DdlDiff.build(
+                originalSegment.getValue(),
+                newSegment.getValue(),
+                ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
         // Run diff with allowRecreateIndexes and allowDropStatements
         List<String> diff =
             ddlDiff.generateDifferenceStatements(
diff --git a/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffTest.java b/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffTest.java
index 9f255fc..4274973 100644
--- a/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffTest.java
+++ b/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffTest.java
@@ -23,7 +23,6 @@
 import static org.junit.Assert.fail;
 
 import com.google.cloud.solutions.spannerddl.parser.ASTddl_statement;
-import com.google.cloud.solutions.spannerddl.parser.ParseException;
 import com.google.common.collect.ImmutableMap;
 import java.util.Arrays;
 import java.util.List;
@@ -32,6 +31,17 @@
 
 public class DdlDiffTest {
 
+  private static final Map<String, Boolean> DEFAULT_OPTIONS =
+      ImmutableMap.of(
+          ALLOW_RECREATE_CONSTRAINTS_OPT,
+          true,
+          ALLOW_DROP_STATEMENTS_OPT,
+          true,
+          ALLOW_RECREATE_INDEXES_OPT,
+          true,
+          DdlDiff.IGNORE_PROTO_BUNDLES_OPT,
+          false);
+
   @Test
   public void parseMultiDdlStatements() throws DdlDiffException {
     String DDL =
@@ -61,7 +71,7 @@ public void parseMultiDdlStatements() throws DdlDiffException {
   }
 
   @Test
-  public void parseCreateTable_anonForeignKey() throws DdlDiffException {
+  public void parseCreateTable_anonForeignKey() {
     try {
       DdlDiff.parseDdl(
           "create table test ("
@@ -70,14 +80,14 @@ public void parseCreateTable_anonForeignKey() throws DdlDiffException {
               + ")"
               + "primary key (intcol ASC)");
       fail("Expected exception not thrown");
-    } catch (IllegalArgumentException e) {
+    } catch (DdlDiffException | IllegalArgumentException e) {
       assertThat(e.getMessage())
           .containsMatch("Can not create diffs when anonymous constraints are used.");
     }
   }
 
   @Test
-  public void parseCreateTable_anonCheckConstraint() throws DdlDiffException {
+  public void parseCreateTable_anonCheckConstraint() {
     try {
       DdlDiff.parseDdl(
           "create table test ("
@@ -86,7 +96,7 @@ public void parseCreateTable_anonCheckConstraint() throws DdlDiffException {
               + ")"
               + "primary key (intcol ASC)");
       fail("Expected exception not thrown");
-    } catch (IllegalArgumentException e) {
+    } catch (DdlDiffException | IllegalArgumentException e) {
       assertThat(e.getMessage())
           .containsMatch("Can not create diffs when anonymous constraints are used.");
     }
@@ -398,7 +408,7 @@ public void generateAlterTable_alterStatementOrdering() throws DdlDiffException
   }
 
   @Test
-  public void parseAlterDatabaseDifferentDbNames() throws ParseException {
+  public void parseAlterDatabaseDifferentDbNames() {
     getDiffCheckDdlDiffException(
         "ALTER DATABASE dbname SET OPTIONS(hello='world');",
         "ALTER DATABASE otherdbname SET OPTIONS(hello='world');",
@@ -445,7 +455,8 @@ public void diffCreateIndexOnlyStoring() throws DdlDiffException {
     assertThat(
             DdlDiff.build(
                     "CREATE INDEX myindex ON mytable ( col1 ) STORING (col2, col3);",
-                    "CREATE INDEX myindex ON mytable ( col1 ) STORING (col3, col4);")
+                    "CREATE INDEX myindex ON mytable ( col1 ) STORING (col3, col4);",
+                    DEFAULT_OPTIONS)
                 .generateDifferenceStatements(
                     ImmutableMap.of(
                         ALLOW_RECREATE_INDEXES_OPT,
@@ -453,6 +464,8 @@ public void diffCreateIndexOnlyStoring() throws DdlDiffException {
                         ALLOW_DROP_STATEMENTS_OPT,
                         false,
                         ALLOW_RECREATE_CONSTRAINTS_OPT,
+                        false,
+                        DdlDiff.IGNORE_PROTO_BUNDLES_OPT,
                         false)))
         .containsExactly(
             "ALTER INDEX myindex DROP STORED COLUMN col2",
@@ -464,7 +477,8 @@ public void diffCreateIndexNotOnlyStoringRecreates() throws DdlDiffException {
     assertThat(
             DdlDiff.build(
                     "CREATE UNIQUE INDEX myindex ON mytable ( col1 ) STORING (col2, col3);",
-                    "CREATE INDEX myindex ON mytable ( col1 ) STORING (col3, col4);")
+                    "CREATE INDEX myindex ON mytable ( col1 ) STORING (col3, col4);",
+                    DEFAULT_OPTIONS)
                 .generateDifferenceStatements(
                     ImmutableMap.of(
                         ALLOW_RECREATE_INDEXES_OPT,
@@ -472,6 +486,8 @@ public void diffCreateIndexNotOnlyStoringRecreates() throws DdlDiffException {
                         ALLOW_DROP_STATEMENTS_OPT,
                         false,
                         ALLOW_RECREATE_CONSTRAINTS_OPT,
+                        false,
+                        DdlDiff.IGNORE_PROTO_BUNDLES_OPT,
                         false)))
         .containsExactly(
             "DROP INDEX myindex",
@@ -479,7 +495,7 @@ public void diffCreateIndexNotOnlyStoringRecreates() throws DdlDiffException {
   }
 
   @Test
-  public void diffCreateIndexNotOnlyStoringThrows() throws DdlDiffException {
+  public void diffCreateIndexNotOnlyStoringThrows() {
     getDiffCheckDdlDiffException(
         "CREATE UNIQUE INDEX myindex ON mytable ( col1 ) STORING (col2, col3);",
         "CREATE INDEX myindex ON mytable ( col1 ) STORING (col3, col4);",
@@ -499,15 +515,23 @@ private static void getDiffCheckDdlDiffException(
 
   private static List<String> getDiff(
       String originalDdl, String newDdl, boolean allowDropStatements) throws DdlDiffException {
-    return DdlDiff.build(originalDdl, newDdl)
-        .generateDifferenceStatements(
-            ImmutableMap.of(
-                ALLOW_RECREATE_CONSTRAINTS_OPT,
-                true,
-                ALLOW_DROP_STATEMENTS_OPT,
-                allowDropStatements,
-                ALLOW_RECREATE_INDEXES_OPT,
-                false));
+    return getDiff(originalDdl, newDdl, allowDropStatements, false);
+  }
+
+  private static List<String> getDiff(
+      String originalDdl, String newDdl, boolean allowDropStatements, boolean ignoreProtoBundles)
+      throws DdlDiffException {
+    Map<String, Boolean> options =
+        ImmutableMap.of(
+            ALLOW_RECREATE_CONSTRAINTS_OPT,
+            true,
+            ALLOW_DROP_STATEMENTS_OPT,
+            allowDropStatements,
+            ALLOW_RECREATE_INDEXES_OPT,
+            false,
+            DdlDiff.IGNORE_PROTO_BUNDLES_OPT,
+            ignoreProtoBundles);
+    return DdlDiff.build(originalDdl, newDdl, options).generateDifferenceStatements(options);
   }
 
   @Test
@@ -516,7 +540,8 @@ public void generateDifferences_dropTables() throws DdlDiffException {
         DdlDiff.build(
             "Create table table1 (col1 int64) primary key (col1);"
                 + "Create table table2 (col2 int64) primary key (col2);",
-            "Create table table1 (col1 int64) primary key (col1);");
+            "Create table table1 (col1 int64) primary key (col1);",
+            DEFAULT_OPTIONS);
 
     assertThat(diff.generateDifferenceStatements(ImmutableMap.of(ALLOW_DROP_STATEMENTS_OPT, true)))
         .containsExactly("DROP TABLE table2");
@@ -530,7 +555,8 @@ public void generateDifferences_dropIndexes() throws DdlDiffException {
         DdlDiff.build(
             "Create index index1 on table1 (col1 desc);"
                 + "Create index index2 on table2 (col2 desc);",
-            "Create index index1 on table1 (col1 desc);");
+            "Create index index1 on table1 (col1 desc);",
+            DEFAULT_OPTIONS);
 
     assertThat(diff.generateDifferenceStatements(ImmutableMap.of(ALLOW_DROP_STATEMENTS_OPT, true)))
         .containsExactly("DROP INDEX index2");
@@ -541,11 +567,18 @@ public void generateDifferences_dropIndexes() throws DdlDiffException {
   @Test
   public void differentIndexesWithNoRecreate() {
     Map<String, Boolean> options =
-        ImmutableMap.of(ALLOW_DROP_STATEMENTS_OPT, false, ALLOW_RECREATE_INDEXES_OPT, false);
+        ImmutableMap.of(
+            ALLOW_DROP_STATEMENTS_OPT,
+            false,
+            ALLOW_RECREATE_INDEXES_OPT,
+            false,
+            DdlDiff.IGNORE_PROTO_BUNDLES_OPT,
+            false);
     try {
       DdlDiff.build(
               "Create unique null_filtered index index1 on table1 (col1 desc)",
-              "Create unique null_filtered index index1 on table1 (col1 asc)")
+              "Create unique null_filtered index index1 on table1 (col1 asc)",
+              options)
           .generateDifferenceStatements(options);
       fail("Expected exception not thrown");
     } catch (DdlDiffException e) {
@@ -554,7 +587,8 @@ public void differentIndexesWithNoRecreate() {
     try {
       DdlDiff.build(
               "Create unique null_filtered index index1 on table1 (col1 desc)",
-              "Create unique null_filtered index index1 on table1 (col2 desc)")
+              "Create unique null_filtered index index1 on table1 (col2 desc)",
+              options)
           .generateDifferenceStatements(options);
       fail("Expected exception not thrown");
     } catch (DdlDiffException e) {
@@ -563,7 +597,8 @@ public void differentIndexesWithNoRecreate() {
     try {
       DdlDiff.build(
               "Create unique null_filtered index index1 on table1 (col1 desc)",
-              "Create index index1 on table1 (col1 desc)")
+              "Create index index1 on table1 (col1 desc)",
+              options)
           .generateDifferenceStatements(options);
       fail("Expected exception not thrown");
     } catch (DdlDiffException e) {
@@ -574,11 +609,18 @@ public void differentIndexesWithNoRecreate() {
   @Test
   public void differentIndexesWithRecreate() throws DdlDiffException {
     Map<String, Boolean> options =
-        ImmutableMap.of(ALLOW_DROP_STATEMENTS_OPT, true, ALLOW_RECREATE_INDEXES_OPT, true);
+        ImmutableMap.of(
+            ALLOW_DROP_STATEMENTS_OPT,
+            true,
+            ALLOW_RECREATE_INDEXES_OPT,
+            true,
+            DdlDiff.IGNORE_PROTO_BUNDLES_OPT,
+            false);
     assertThat(
             DdlDiff.build(
                     "Create unique null_filtered index index1 on table1 (col1 desc)",
-                    "Create unique null_filtered index index1 on table1 (col1 asc)")
+                    "Create unique null_filtered index index1 on table1 (col1 asc)",
+                    options)
                 .generateDifferenceStatements(options))
         .isEqualTo(
             Arrays.asList(
@@ -587,7 +629,8 @@ public void differentIndexesWithRecreate() throws DdlDiffException {
     assertThat(
             DdlDiff.build(
                     "Create unique null_filtered index index1 on table1 ( col1 desc )",
-                    "Create unique null_filtered index index1 on table1 ( col2 desc )")
+                    "Create unique null_filtered index index1 on table1 ( col2 desc )",
+                    options)
                 .generateDifferenceStatements(options))
         .isEqualTo(
             Arrays.asList(
@@ -596,9 +639,27 @@ public void differentIndexesWithRecreate() throws DdlDiffException {
     assertThat(
             DdlDiff.build(
                     "Create unique null_filtered index index1 on table1 ( col1 desc )",
-                    "Create index index1 on table1 ( col1 desc )")
+                    "Create index index1 on table1 ( col1 desc )",
+                    options)
                 .generateDifferenceStatements(options))
         .isEqualTo(
             Arrays.asList("DROP INDEX index1", "CREATE INDEX index1 ON table1 ( col1 DESC )"));
   }
+
+  @Test
+  public void ignoreProtoBundles_throwsExceptionWhenNotIgnoring() {
+    try {
+      getDiff("CREATE PROTO BUNDLE (a,b,c)", "", false, false);
+      fail("Expected exception not thrown");
+    } catch (UnsupportedOperationException e) {
+      assertThat(e.getMessage()).isEqualTo("Not Implemented");
+    } catch (DdlDiffException e) {
+      fail("Unexpected DdlDiffException: " + e);
+    }
+  }
+
+  @Test
+  public void ignoreProtoBundles_ignoresWhenFlagIsSet() throws DdlDiffException {
+    assertThat(getDiff("", "CREATE PROTO BUNDLE (a,b,c)", false, true)).isEmpty();
+  }
 }
diff --git a/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffValidationTest.java b/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffValidationTest.java
index be58a0e..8d9e737 100644
--- a/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffValidationTest.java
+++ b/src/test/java/com/google/cloud/solutions/spannerddl/diff/DdlDiffValidationTest.java
@@ -19,6 +19,7 @@
 import static com.google.common.truth.Truth.assertThat;
 import static org.junit.Assert.fail;
 
+import com.google.common.collect.ImmutableMap;
 import org.junit.Test;
 
 public class DdlDiffValidationTest {
@@ -28,7 +29,7 @@ public void validateForeignKey_missingReferencedTable() {
     String ddl =
         "CREATE TABLE test1 ( col1 INT64, col2 STRING(100), CONSTRAINT fk_in_table FOREIGN KEY (col2) REFERENCES othertable (othercol) ) PRIMARY KEY (col1);";
     try {
-      DdlDiff.validateDdl(ddl);
+      DdlDiff.validateDdl(ddl, ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
       fail("Expected DdlDiffException");
     } catch (DdlDiffException e) {
       assertThat(e.getMessage())
@@ -43,7 +44,7 @@ public void validateForeignKey_existingTable() {
         "CREATE TABLE test1 ( col1 INT64, col2 STRING(100), CONSTRAINT fk_in_table FOREIGN KEY (col2) REFERENCES othertable (othercol) ) PRIMARY KEY (col1);"
             + "CREATE table othertable ( othercol INT64, col4 STRING(100) ) PRIMARY KEY (othercol);";
     try {
-      DdlDiff.validateDdl(ddl);
+      DdlDiff.validateDdl(ddl, ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
     } catch (DdlDiffException e) {
       throw new RuntimeException(e);
     }
@@ -55,7 +56,7 @@ public void validateForeignKey_missingReferencedColumn() {
         "CREATE TABLE othertable (othercol STRING(100)) PRIMARY KEY (othercol); "
             + "CREATE TABLE test1 ( col1 INT64, col2 STRING(100), CONSTRAINT fk_in_table FOREIGN KEY (col2) REFERENCES othertable (missing_col) ) PRIMARY KEY (col1);";
     try {
-      DdlDiff.validateDdl(ddl);
+      DdlDiff.validateDdl(ddl, ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
       fail("Expected DdlDiffException");
     } catch (DdlDiffException e) {
       assertThat(e.getMessage())
@@ -70,7 +71,7 @@ public void validateForeignKey_existingReferencedColumn() {
         "CREATE TABLE othertable ( othercol STRING(100), existing_col INT64 ) PRIMARY KEY (othercol); "
             + "CREATE TABLE test1 ( col1 INT64, col2 STRING(100), CONSTRAINT fk_in_table FOREIGN KEY (col2) REFERENCES othertable (existing_col) ) PRIMARY KEY (col1);";
     try {
-      DdlDiff.validateDdl(ddl);
+      DdlDiff.validateDdl(ddl, ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
     } catch (DdlDiffException e) {
       throw new RuntimeException(e);
     }
@@ -80,7 +81,7 @@ public void validateForeignKey_existingReferencedColumn() {
   public void validateIndex_missingTable() {
     String ddl = "CREATE INDEX myindex ON mytable (col1);";
     try {
-      DdlDiff.validateDdl(ddl);
+      DdlDiff.validateDdl(ddl, ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
       fail("Expected DdlDiffException");
     } catch (DdlDiffException e) {
       assertThat(e.getMessage())
@@ -94,7 +95,7 @@ public void validateIndex_existingTable() {
         "CREATE TABLE mytable ( col1 INT64, col2 STRING(100) ) PRIMARY KEY (col1); "
             + "CREATE INDEX myindex ON mytable (col1);";
     try {
-      DdlDiff.validateDdl(ddl);
+      DdlDiff.validateDdl(ddl, ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
     } catch (DdlDiffException e) {
       throw new RuntimeException(e);
     }
@@ -105,7 +106,7 @@ public void validateIndex_missingColumn() {
     String ddl =
         "CREATE TABLE mytable (col1 INT64) PRIMARY KEY (col1); CREATE INDEX myindex ON mytable (missing_col);";
     try {
-      DdlDiff.validateDdl(ddl);
+      DdlDiff.validateDdl(ddl, ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
       fail("Expected DdlDiffException");
     } catch (DdlDiffException e) {
       assertThat(e.getMessage())
@@ -119,7 +120,7 @@ public void validateIndex_existingColumn() {
     String ddl =
         "CREATE TABLE mytable (col1 INT64, existing_col INT64 ) PRIMARY KEY (col1); CREATE INDEX myindex ON mytable (existing_col);";
     try {
-      DdlDiff.validateDdl(ddl);
+      DdlDiff.validateDdl(ddl, ImmutableMap.of(DdlDiff.IGNORE_PROTO_BUNDLES_OPT, false));
     } catch (DdlDiffException e) {
       throw new RuntimeException(e);
     }
diff --git a/src/test/resources/ddlParserUnsupported.txt b/src/test/resources/ddlParserUnsupported.txt
index d1bf7af..265378c 100644
--- a/src/test/resources/ddlParserUnsupported.txt
+++ b/src/test/resources/ddlParserUnsupported.txt
@@ -139,21 +139,21 @@ ALTER TABLE table_name DROP SYNONYM table_name
 
 ALTER TABLE table_name ADD SYNONYM table_name
 
-== Test 17a // TODO Create proto bundle
-
-CREATE PROTO BUNDLE (proto.path.name, other.proto.path)
-
-== Test 17b Alter proto bundle INSERT
-
-ALTER PROTO BUNDLE INSERT (proto.path.name, other.proto.path)
-
-== Test 17c Alter proto bundle UPDATE
-
-ALTER PROTO BUNDLE UPDATE (proto.path.name, other.proto.path)
-
-== Test 17d Alter proto bundle DELETE
-
-ALTER PROTO BUNDLE DELETE (proto.path.name, other.proto.path)
+# == Test 17a // TODO Create proto bundle. Commented out to allow user to ignore proto bundles when parsing
+#
+# CREATE PROTO BUNDLE (proto.path.name, other.proto.path)
+#
+# == Test 17b Alter proto bundle INSERT
+#
+# ALTER PROTO BUNDLE INSERT (proto.path.name, other.proto.path)
+#
+# == Test 17c Alter proto bundle UPDATE
+#
+# ALTER PROTO BUNDLE UPDATE (proto.path.name, other.proto.path)
+#
+# == Test 17d Alter proto bundle DELETE
+#
+# ALTER PROTO BUNDLE DELETE (proto.path.name, other.proto.path)
 
 == Test 18a alter search index