diff --git a/src/PharBuilder.php b/src/PharBuilder.php
index adbaacf..2eb818a 100644
--- a/src/PharBuilder.php
+++ b/src/PharBuilder.php
@@ -103,9 +103,15 @@ public function build($filename, $stub) {
                 $phar->setSignatureAlgorithm($this->selectSignatureType());
             }
 
-            $basedir = $this->basedir ? $this->basedir : $this->directories[0];
+            $basedir = $this->basedir ?: $this->directories[0];
             foreach($this->directories as $directory) {
-                $phar->buildFromIterator($this->scanner->__invoke($directory), $basedir);
+                if (file_exists("$directory/")) {
+                    $phar->buildFromIterator($this->scanner->__invoke($directory), $basedir);
+                } else {
+                    $comparator = new PathComparator(array($basedir, $directory));
+                    $localName = str_replace($comparator->getCommonBase().'/', '', $directory);
+                    $phar->addFile($directory, $localName);
+                }
             }
 
             if ($this->compression !== \Phar::NONE) {