diff --git a/.pre-commit-hooks.yaml b/.pre-commit-hooks.yaml
index 7a3b380..8b123dc 100644
--- a/.pre-commit-hooks.yaml
+++ b/.pre-commit-hooks.yaml
@@ -192,3 +192,9 @@
     language: python
     types: [text]
     stages: [commit, push, manual]
+-   id: run-sub-hooks
+    name: Run Subdirectory Hooks
+    description: Runs subprocess with alternative pre-commit configuration.
+    entry: run-sub-hooks
+    language: python
+    verbose: true
diff --git a/README.md b/README.md
index b0ea69b..e5194f0 100644
--- a/README.md
+++ b/README.md
@@ -95,6 +95,10 @@ Add this to your `.pre-commit-config.yaml`
     - `--no-sort-keys` - when autofixing, retain the original key ordering (instead of sorting the keys)
     - `--top-keys comma,separated,keys` - Keys to keep at the top of mappings.
 - `requirements-txt-fixer` - Sorts entries in requirements.txt and removes incorrect entry for `pkg-resources==0.0.0`
+- `run-sub-hooks` - Runs subprocess with alternative pre-commit configuration.
+    - `--target` - target directory (doesn't have to be repository root
+    - `--config ...` - Control
+- `requirements-txt-fixer` - Sorts entries in requirements.txt and removes incorrect entry for `pkg-resources==0.0.0`
 - `sort-simple-yaml` - Sorts simple YAML files which consist only of top-level
   keys, preserving comments and blocks.
 
diff --git a/pre_commit_hooks/run_sub_hooks.py b/pre_commit_hooks/run_sub_hooks.py
new file mode 100644
index 0000000..53946d3
--- /dev/null
+++ b/pre_commit_hooks/run_sub_hooks.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+"""
+Run pre-commit with different config under pre-commit hook.
+
+Initial idea & code:
+https://github.com/pre-commit/pre-commit/issues/731#issuecomment-376945745
+"""
+import argparse
+import os
+import subprocess
+import sys
+from typing import List
+from typing import Optional
+from typing import Sequence
+
+
+def all_files(target):  # type: (str) -> List[str]
+    return sum(
+        (
+            [os.path.join(dirpath, file) for file in filenames]
+            for (dirpath, dirnames, filenames) in os.walk(target)
+        ),
+        [],
+    )
+
+
+def main(args=None):  # type: (Optional[Sequence[str]]) -> int
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '-t',
+        '--target',
+        dest='target',
+        help='target directory to which pre-commit should be limited',
+    )
+    parser.add_argument(
+        '-c',
+        '--config',
+        dest='config',
+        default='.pre-commit-config.yaml',
+        help='config in relation to target directory',
+    )
+    parser.add_argument('--all-files', action='store_true')
+    options, args = parser.parse_known_args(args)
+
+    def is_default(arg):  # type: (str) -> bool
+        return getattr(options, arg) == parser.get_default(arg)
+
+    if is_default('target') and is_default('config'):
+        parser.error('`target` or `config` has to be specified')
+
+    precommit_cfg = os.path.join(options.target, options.config)
+    cmd = ['pre-commit', 'run', '--config', precommit_cfg, '--files']
+
+    if options.all_files:
+        if options.target == '.':
+            args.insert(0, '--all-files')
+        else:
+            args.extend(all_files(options.target))
+
+    return subprocess.call(cmd + args, stdout=sys.stdout, stderr=sys.stderr)
+
+
+if __name__ == '__main__':
+    exit(main())
diff --git a/setup.cfg b/setup.cfg
index 12c2b16..041d070 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -61,6 +61,7 @@ console_scripts =
     no-commit-to-branch = pre_commit_hooks.no_commit_to_branch:main
     pretty-format-json = pre_commit_hooks.pretty_format_json:main
     requirements-txt-fixer = pre_commit_hooks.requirements_txt_fixer:main
+    run-sub-hooks = pre_commit_hooks.run_sub_hooks:main
     sort-simple-yaml = pre_commit_hooks.sort_simple_yaml:main
     trailing-whitespace-fixer = pre_commit_hooks.trailing_whitespace_fixer:main
 
diff --git a/tests/run_sub_hooks_test.py b/tests/run_sub_hooks_test.py
new file mode 100644
index 0000000..8cf9794
--- /dev/null
+++ b/tests/run_sub_hooks_test.py
@@ -0,0 +1,55 @@
+import re
+
+import pytest
+
+from pre_commit_hooks.run_sub_hooks import main
+
+
+@pytest.fixture
+def temp_sub_dir(temp_git_dir):
+    """Temporary git subdirectory with pre-commit config inside of it"""
+    with temp_git_dir.as_cwd():
+        sub_dir = temp_git_dir.mkdir('subdir')
+        sub_dir.join('.pre-commit-config.yaml').write(
+            """\
+repos:
+        -   repo: https://github.com/pre-commit/pre-commit-hooks
+            rev: v2.0.0
+            hooks:
+            -   id: trailing-whitespace\
+"""
+        )
+        yield sub_dir
+
+
+INFO_PATTERN = re.compile(r'^\s*(\[INFO\] [^\n]+\n)+', flags=re.M)
+
+
+def test_clean_run(temp_sub_dir, capfd):
+    assert main(['--target', str(temp_sub_dir), '--all-files']) == 0
+    captured = capfd.readouterr()
+    assert (  # noqa: E501
+        INFO_PATTERN.sub('', captured.out) ==
+        """\
+Trim Trailing Whitespace.................................................Passed
+"""
+    )
+    assert captured.err == ''
+
+
+def test_only_sub_dir_files_when_all_files(temp_git_dir, temp_sub_dir, capfd):
+    temp_git_dir.join('file1.yaml').write('some trailing whitespace ->    ')
+    temp_sub_dir.join('file2.yaml').write('some trailing whitespace ->    ')
+    assert main(['--target', str(temp_sub_dir), '--all-files']) == 1
+    captured = capfd.readouterr()
+    assert (  # noqa: E501
+        INFO_PATTERN.sub('', captured.out) ==
+        """\
+Trim Trailing Whitespace.................................................Failed
+hookid: trailing-whitespace
+
+Fixing subdir/file2.yaml
+
+"""
+    )
+    assert captured.err == ''