diff --git a/src/filterFiles.ts b/src/filterFiles.ts
index 60983b32..f5494d34 100644
--- a/src/filterFiles.ts
+++ b/src/filterFiles.ts
@@ -1,17 +1,49 @@
 import { join } from "./path"
 import { removeSync } from "fs-extra"
 import klawSync from "klaw-sync"
+import { spawnSafeSync } from "./spawnSafe"
+
+const gitExcludePaths = (dir: string): RegExp => {
+  const anyRegExp = (regExps: RegExp[], flags?: string): RegExp =>
+    regExps.length <= 0
+      ? /(?!)/ // never matches
+      : new RegExp(regExps.map(regExp => regExp.source).join("|"), flags)
+  const escapeRegExp = (str: string): string =>
+    str.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&")
+  const gitExcludeFilesResult = spawnSafeSync(
+    "git",
+    ["ls-files", "-o", "-i", "--exclude-standard"],
+    {
+      cwd: dir,
+      throwOnError: false,
+      logStdErrOnError: false,
+    },
+  )
+  return anyRegExp(
+    gitExcludeFilesResult.status === 0
+      ? gitExcludeFilesResult.stdout
+          .toString()
+          .split(/\n/g)
+          .map(escapeRegExp)
+          .map(escaped => new RegExp(escaped))
+      : [],
+    "i",
+  )
+}
 
 export function removeIgnoredFiles(
   dir: string,
   includePaths: RegExp,
   excludePaths: RegExp,
 ) {
+  const gitIgnoredPaths = gitExcludePaths(dir)
   klawSync(dir, { nodir: true })
     .map(item => item.path.slice(`${dir}/`.length))
     .filter(
       relativePath =>
-        !relativePath.match(includePaths) || relativePath.match(excludePaths),
+        !relativePath.match(includePaths) ||
+        relativePath.match(excludePaths) ||
+        relativePath.match(gitIgnoredPaths),
     )
     .forEach(relativePath => removeSync(join(dir, relativePath)))
 }
diff --git a/src/index.ts b/src/index.ts
index ae7bb733..6aa117a0 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -124,5 +124,9 @@ Usage:
      ${chalk.bold("--case-sensitive-path-filtering")}
 
          Make regexps used in --include or --exclude filters case-sensitive.
+
+     ${chalk.bold("--patch-dir")}
+
+         Specify the name for the directory in which to put the patch files.
 `)
 }