diff --git a/pre_commit/commands/run.py b/pre_commit/commands/run.py
index 6a72149e..59901388 100644
--- a/pre_commit/commands/run.py
+++ b/pre_commit/commands/run.py
@@ -129,7 +129,7 @@ def _run_single_hook(classifier, hook, args, skips, cols, use_color):
     diff_after = cmd_output_b('git', 'diff', '--no-ext-diff', retcode=None)
 
     file_modifications = diff_before != diff_after
-    modified_ok = args.modified_files_ok
+    modified_ok = args.modified_files_ok or args.add_modified
 
     # If the hook makes changes, fail the commit
     if not modified_ok and file_modifications:
@@ -169,6 +169,10 @@ def _run_single_hook(classifier, hook, args, skips, cols, use_color):
             output.write_line(out.strip(), logfile_name=hook.log_file)
         output.write_line()
 
+    if file_modifications and modified_ok:
+        output.write_line('Adding modified files to index\n')
+        git.add_all()
+
     return retcode
 
 
diff --git a/pre_commit/git.py b/pre_commit/git.py
index 3ee9ca3a..37e45e38 100644
--- a/pre_commit/git.py
+++ b/pre_commit/git.py
@@ -192,3 +192,8 @@ def check_for_cygwin_mismatch():
                     exe_type[is_cygwin_python], exe_type[is_cygwin_git],
                 ),
             )
+
+
+def add_all(repo='.'):
+    cmd = ('git', 'add', '.')
+    cmd_output(*cmd, cwd=repo)
diff --git a/pre_commit/main.py b/pre_commit/main.py
index ade17a51..e3242492 100644
--- a/pre_commit/main.py
+++ b/pre_commit/main.py
@@ -108,6 +108,15 @@ def _add_run_options(parser):
              'Equivalent to setting the environment variable '
              'PRE_COMMIT_MODIFIED_FILES_OK=true.',
     )
+    parser.add_argument(
+        '--add-modified', action='store_true',
+        default='PRE_COMMIT_ADD_MODIFIED_FILES' in os.environ,
+        help='Any file modifications made by hooks will be automatically '
+             'added to the index unless any hook fails. When set, file '
+             "modification by hooks won't be equated with failure (same as if "
+             '--modified-files-ok is set). Equivalent to setting the '
+             'environment variable PRE_COMMIT_ADD_MODIFIED_FILES=true.',
+    )
     mutex_group = parser.add_mutually_exclusive_group(required=False)
     mutex_group.add_argument(
         '--all-files', '-a', action='store_true', default=False,
diff --git a/testing/util.py b/testing/util.py
index fa706b2f..6a6ba54b 100644
--- a/testing/util.py
+++ b/testing/util.py
@@ -108,6 +108,7 @@ def run_opts(
         show_diff_on_failure=False,
         commit_msg_filename='',
         modified_files_ok=False,
+        add_modified=False,
 ):
     # These are mutually exclusive
     assert not (all_files and files)
@@ -123,6 +124,7 @@ def run_opts(
         show_diff_on_failure=show_diff_on_failure,
         commit_msg_filename=commit_msg_filename,
         modified_files_ok=modified_files_ok,
+        add_modified=add_modified,
     )