diff --git a/autoflake.py b/autoflake.py
index 77a5916..70a5aa5 100755
--- a/autoflake.py
+++ b/autoflake.py
@@ -331,7 +331,9 @@ def filter_code(source, additional_imports=None,
                 expand_star_imports=False,
                 remove_all_unused_imports=False,
                 remove_duplicate_keys=False,
-                remove_unused_variables=False):
+                remove_unused_variables=False,
+                ignore_init_module_imports=False,
+                ):
     """Yield code with unused imports removed."""
     imports = SAFE_IMPORTS
     if additional_imports:
@@ -340,8 +342,11 @@ def filter_code(source, additional_imports=None,
 
     messages = check(source)
 
-    marked_import_line_numbers = frozenset(
-        unused_import_line_numbers(messages))
+    if ignore_init_module_imports:
+        marked_import_line_numbers = frozenset()
+    else:
+        marked_import_line_numbers = frozenset(
+            unused_import_line_numbers(messages))
     marked_unused_module = collections.defaultdict(lambda: [])
     for line_number, module_name in unused_import_module_name(messages):
         marked_unused_module[line_number].append(module_name)
@@ -589,7 +594,7 @@ def get_line_ending(line):
 
 def fix_code(source, additional_imports=None, expand_star_imports=False,
              remove_all_unused_imports=False, remove_duplicate_keys=False,
-             remove_unused_variables=False):
+             remove_unused_variables=False, ignore_init_module_imports=False):
     """Return code with all filtering run on it."""
     if not source:
         return source
@@ -608,7 +613,9 @@ def fix_code(source, additional_imports=None, expand_star_imports=False,
                     expand_star_imports=expand_star_imports,
                     remove_all_unused_imports=remove_all_unused_imports,
                     remove_duplicate_keys=remove_duplicate_keys,
-                    remove_unused_variables=remove_unused_variables))))
+                    remove_unused_variables=remove_unused_variables,
+                    ignore_init_module_imports=ignore_init_module_imports,
+                    ))))
 
         if filtered_source == source:
             break
@@ -625,13 +632,20 @@ def fix_file(filename, args, standard_out):
 
     original_source = source
 
+    if args.ignore_init_module_imports and filename.endswith('__init__.py'):
+        ignore_init_module_imports = True
+    else:
+        ignore_init_module_imports = False
+
     filtered_source = fix_code(
         source,
         additional_imports=args.imports.split(',') if args.imports else None,
         expand_star_imports=args.expand_star_imports,
         remove_all_unused_imports=args.remove_all_unused_imports,
         remove_duplicate_keys=args.remove_duplicate_keys,
-        remove_unused_variables=args.remove_unused_variables)
+        remove_unused_variables=args.remove_unused_variables,
+        ignore_init_module_imports=ignore_init_module_imports,
+        )
 
     if original_source != filtered_source:
         if args.in_place:
@@ -791,6 +805,9 @@ def _main(argv, standard_out, standard_error):
     parser.add_argument('--remove-all-unused-imports', action='store_true',
                         help='remove all unused imports (not just those from '
                              'the standard library)')
+    parser.add_argument('--ignore-init-module-imports', action='store_true',
+                        help='exclude __init__.py when removing unused '
+                             'imports')
     parser.add_argument('--remove-duplicate-keys', action='store_true',
                         help='remove all duplicate keys in objects')
     parser.add_argument('--remove-unused-variables', action='store_true',
diff --git a/test_autoflake.py b/test_autoflake.py
index 919a81a..8cdd710 100755
--- a/test_autoflake.py
+++ b/test_autoflake.py
@@ -501,6 +501,41 @@ def foo():
 """
         self.assertEqual(line, ''.join(autoflake.filter_code(line)))
 
+    def test_with_ignore_init_module_imports_flag(self):
+        # Need a temp directory in order to specify file name as __init__.py
+        temp_directory = tempfile.mkdtemp(dir='.')
+        temp_file = os.path.join(temp_directory, '__init__.py')
+        try:
+            with open(temp_file, 'w') as output:
+                output.write('import re\n')
+
+            p = subprocess.Popen(
+                list(AUTOFLAKE_COMMAND) +
+                ['--ignore-init-module-imports', temp_file],
+                stdout=subprocess.PIPE)
+            result = p.communicate()[0].decode('utf-8')
+
+            self.assertNotIn('import re', result)
+        finally:
+            shutil.rmtree(temp_directory)
+
+    def test_without_ignore_init_module_imports_flag(self):
+        # Need a temp directory in order to specify file name as __init__.py
+        temp_directory = tempfile.mkdtemp(dir='.')
+        temp_file = os.path.join(temp_directory, '__init__.py')
+        try:
+            with open(temp_file, 'w') as output:
+                output.write('import re\n')
+
+            p = subprocess.Popen(
+                list(AUTOFLAKE_COMMAND) + [temp_file],
+                stdout=subprocess.PIPE)
+            result = p.communicate()[0].decode('utf-8')
+
+            self.assertIn('import re', result)
+        finally:
+            shutil.rmtree(temp_directory)
+
     def test_fix_code(self):
         self.assertEqual(
             """\