diff --git a/ament_clang_tidy/ament_clang_tidy/main.py b/ament_clang_tidy/ament_clang_tidy/main.py
index f2b7eeab6..f0e6c6419 100755
--- a/ament_clang_tidy/ament_clang_tidy/main.py
+++ b/ament_clang_tidy/ament_clang_tidy/main.py
@@ -17,6 +17,7 @@
 import argparse
 from collections import defaultdict
 import copy
+import glob
 import json
 from multiprocessing.pool import ThreadPool
 import os
@@ -84,11 +85,18 @@ def main(argv=sys.argv[1:]):
     parser.add_argument(
         '--packages-select', nargs='*', metavar='PKG_NAME',
         help='Only process a subset of packages')
+    parser.add_argument(
+        '--exclude', default=[], nargs='*', help='Filenames to exclude')
     parser.add_argument(
         '--xunit-file',
         help='Generate a xunit compliant XML file')
     args = parser.parse_args(argv)
 
+    excludes = []
+    for exclude_pattern in args.exclude:
+        excludes.extend(glob.glob(exclude_pattern))
+    excludes = {os.path.realpath(x) for x in excludes}
+
     if args.config_file is not None and not os.path.exists(args.config_file):
         print("Could not find config file '%s'" % args.config_file,
               file=sys.stderr)
@@ -162,6 +170,14 @@ def is_gtest_source(file_name):
         def is_unittest_source(package, file_path):
             return ('%s/test/' % package) in file_path
 
+        def is_protobuf_source(file_name):
+            if(file_name.endswith('.pb.cc') or file_name.endswith('.pb.h')):
+                return True
+            return False
+
+        def is_excluded(file_path):
+            return file_path in excludes
+
         def start_subprocess(full_cmd):
             output = ''
             try:
@@ -188,6 +204,14 @@ def start_subprocess(full_cmd):
             if is_unittest_source(package_name, item['file']):
                 continue
 
+            # exclude auto-generated protobuf sources from being checked by clang-tidy
+            if is_protobuf_source(os.path.basename(item['file'])):
+                continue
+
+            # exclude files that are explicitly excluded
+            if is_excluded(item['file']):
+                continue
+
             files.append(item['file'])
             full_cmd = cmd + [item['file']]
             async_outputs.append(pool.apply_async(start_subprocess, (full_cmd,)))
diff --git a/ament_clang_tidy/doc/index.rst b/ament_clang_tidy/doc/index.rst
index d8255f9a1..c2bdd6283 100644
--- a/ament_clang_tidy/doc/index.rst
+++ b/ament_clang_tidy/doc/index.rst
@@ -19,10 +19,11 @@ have already been installed. ``compile_commands.json`` files should have already
     ament_clang_tidy [-h] [--config path] [--explain-config]
                      [--export-fixes EXPORT_FIXES] [--fix-errors]
                      [--header-filter HEADER_FILTER] [--quiet]
-                     [--system-headers] [--jobs N]
-                     [--packages-select [PKG_NAME [PKG_NAME ...]]]
+                     [--system-headers] [--jobs JOBS]
+                     [--packages-select [PKG_NAME ...]]
+                     [--exclude [EXCLUDE ...]] 
                      [--xunit-file XUNIT_FILE]
-                     [paths [paths ...]]
+                     [paths ...]
 
 If ``<paths>`` is a directory, it will be recursively searched for
 "compile_commands.json" files (this is usually the ``build`` directory of a
@@ -56,6 +57,8 @@ parallel.
 The ``--packages-select`` option will filter the "compile_commands.json" files
 to just those generated by specific ROS packages.
 
+The ``--exclude`` option will exclude the specified patterns.
+
 The ``--xunit-file`` option will generate a xunit compliant XML file when
 supplied with a file name.
 
diff --git a/ament_cmake_clang_tidy/cmake/ament_clang_tidy.cmake b/ament_cmake_clang_tidy/cmake/ament_clang_tidy.cmake
index 95df6abe6..0927723a9 100644
--- a/ament_cmake_clang_tidy/cmake/ament_clang_tidy.cmake
+++ b/ament_cmake_clang_tidy/cmake/ament_clang_tidy.cmake
@@ -25,6 +25,8 @@
 #
 # :param TESTNAME: the name of the test, default: "clang_tidy"
 # :type TESTNAME: string
+# :param EXCLUDE: an optional list of exclude directories or files for flake8
+# :type EXCLUDE: list
 # :param CONFIG_FILE: the path of the configuration file for clang-tidy to consider
 # :type CONFIG_FILE: string
 # :param ARGN: the files or directories to check
@@ -35,7 +37,7 @@
 # @public
 #
 function(ament_clang_tidy)
-  cmake_parse_arguments(ARG "" "TESTNAME;CONFIG_FILE;TIMEOUT;HEADER_FILTER;JOBS" "" ${ARGN})
+  cmake_parse_arguments(ARG "" "TESTNAME;EXCLUDE;CONFIG_FILE;TIMEOUT;HEADER_FILTER;JOBS" "" ${ARGN})
   if(NOT ARG_TESTNAME)
     set(ARG_TESTNAME "clang_tidy")
   endif()
@@ -49,6 +51,10 @@ function(ament_clang_tidy)
   set(cmd "${ament_clang_tidy_BIN}" "--xunit-file" "${result_file}")
   list(APPEND cmd ${ARG_UNPARSED_ARGUMENTS})
 
+  if(ARG_EXCLUDE)
+    list(APPEND cmd "--exclude" "${ARG_EXCLUDE}")
+  endif()
+
   if(ARG_CONFIG_FILE)
     list(APPEND cmd "--config" "${ARG_CONFIG_FILE}")
   elseif(DEFINED ament_cmake_clang_tidy_CONFIG_FILE)
diff --git a/ament_cmake_clang_tidy/cmake/ament_cmake_clang_tidy_lint_hook.cmake b/ament_cmake_clang_tidy/cmake/ament_cmake_clang_tidy_lint_hook.cmake
index 06b08bace..c9d7da719 100644
--- a/ament_cmake_clang_tidy/cmake/ament_cmake_clang_tidy_lint_hook.cmake
+++ b/ament_cmake_clang_tidy/cmake/ament_cmake_clang_tidy_lint_hook.cmake
@@ -24,5 +24,5 @@ file(GLOB_RECURSE _source_files FOLLOW_SYMLINKS
 )
 if(_source_files)
   message(STATUS "Added test 'clang_tidy' to check C / C++ code style")
-  ament_clang_tidy("${CMAKE_CURRENT_BINARY_DIR}")
+  ament_clang_tidy(EXCLUDE ${AMENT_LINT_AUTO_FILE_EXCLUDE} "${CMAKE_CURRENT_BINARY_DIR}")
 endif()