diff --git a/features/checksum-core.feature b/features/checksum-core.feature
index fffcc0b2..f58e26f0 100644
--- a/features/checksum-core.feature
+++ b/features/checksum-core.feature
@@ -147,6 +147,10 @@ Feature: Validate checksums for WordPress install
 
   Scenario: Verify core checksums when extra files are included in WordPress root and --include-root is passed
     Given a WP install
+    And a .htaccess file:
+      """
+      # BEGIN WordPress
+      """
     And a extra-file.php file:
       """
       hello world
@@ -169,6 +173,10 @@ Feature: Validate checksums for WordPress install
       """
       Warning: File should not exist: extra-file.php
       """
+    And STDERR should not contain:
+      """
+      Warning: File should not exist: .htaccess
+      """
     And STDERR should not contain:
       """
       Warning: File should not exist: wp-content/unknown-file.php
diff --git a/src/Checksum_Core_Command.php b/src/Checksum_Core_Command.php
index eed09828..a6d76cba 100644
--- a/src/Checksum_Core_Command.php
+++ b/src/Checksum_Core_Command.php
@@ -151,7 +151,7 @@ public function __invoke( $args, $assoc_args ) {
 	 */
 	protected function filter_file( $filepath ) {
 		if ( true === $this->include_root ) {
-			return ( 1 !== preg_match( '/^(wp-config\.php$|wp-content\/)/', $filepath ) );
+			return ( 1 !== preg_match( '/^(\.htaccess$|wp-config\.php$|wp-content\/)/', $filepath ) );
 		}
 
 		return ( 0 === strpos( $filepath, 'wp-admin/' )