diff --git a/src/Composer/Autoload/AutoloadGenerator.php b/src/Composer/Autoload/AutoloadGenerator.php
index bac2c9852..636c309e2 100644
--- a/src/Composer/Autoload/AutoloadGenerator.php
+++ b/src/Composer/Autoload/AutoloadGenerator.php
@@ -450,12 +450,19 @@ FOOTER;
             if (!isset($autoload[$type]) || !is_array($autoload[$type])) {
                 continue;
             }
-            if (null !== $package->getTargetDir() && $package !== $mainPackage) {
+            if ($type !== 'files' && null !== $package->getTargetDir() && $package !== $mainPackage) {
                 $installPath = substr($installPath, 0, -strlen('/'.$package->getTargetDir()));
             }
 
             foreach ($autoload[$type] as $namespace => $paths) {
                 foreach ((array) $paths as $path) {
+
+                    // remove target-dir from file paths
+                    if ($type === 'files' && !is_readable($installPath.$path)) {
+	                    $targetDir = str_replace('\\<dirsep\\>', '[\\\\/]', preg_quote(str_replace(array('/', '\\'), '<dirsep>', $package->getTargetDir())));
+                        $path = ltrim(preg_replace('{^'.$targetDir.'}', '', ltrim($path, '\\/')), '\\/');
+                    }
+
                     // remove target-dir from classmap entries of the root package
                     if ($type === 'classmap' && $package === $mainPackage && $package->getTargetDir()) {
                         $targetDir = str_replace('\\<dirsep\\>', '[\\\\/]', preg_quote(str_replace(array('/', '\\'), '<dirsep>', $package->getTargetDir())));
diff --git a/tests/Composer/Test/Autoload/AutoloadGeneratorTest.php b/tests/Composer/Test/Autoload/AutoloadGeneratorTest.php
index 233b399af..02ad8a6ee 100644
--- a/tests/Composer/Test/Autoload/AutoloadGeneratorTest.php
+++ b/tests/Composer/Test/Autoload/AutoloadGeneratorTest.php
@@ -64,7 +64,8 @@ class AutoloadGeneratorTest extends TestCase
         $this->im->expects($this->any())
             ->method('getInstallPath')
             ->will($this->returnCallback(function ($package) use ($that) {
-                return $that->vendorDir.'/'.$package->getName();
+                $targetDir = $package->getTargetDir();
+                return $that->vendorDir.'/'.$package->getName() . ($targetDir ? '/'.$targetDir : '');
             }));
         $this->repository = $this->getMock('Composer\Repository\RepositoryInterface');
 
@@ -318,8 +319,11 @@ class AutoloadGeneratorTest extends TestCase
         $packages = array();
         $packages[] = $a = new Package('a/a', '1.0', '1.0');
         $packages[] = $b = new Package('b/b', '1.0', '1.0');
+        $packages[] = $c = new Package('c/c', '1.0', '1.0');
         $a->setAutoload(array('files' => array('test.php')));
         $b->setAutoload(array('files' => array('test2.php')));
+        $c->setAutoload(array('files' => array('test3.php', 'foo/bar/test4.php')));
+        $c->setTargetDir('foo/bar');
 
         $this->repository->expects($this->once())
             ->method('getPackages')
@@ -327,8 +331,11 @@ class AutoloadGeneratorTest extends TestCase
 
         $this->fs->ensureDirectoryExists($this->vendorDir.'/a/a');
         $this->fs->ensureDirectoryExists($this->vendorDir.'/b/b');
+        $this->fs->ensureDirectoryExists($this->vendorDir.'/c/c/foo/bar');
         file_put_contents($this->vendorDir.'/a/a/test.php', '<?php function testFilesAutoloadGeneration1() {}');
         file_put_contents($this->vendorDir.'/b/b/test2.php', '<?php function testFilesAutoloadGeneration2() {}');
+        file_put_contents($this->vendorDir.'/c/c/foo/bar/test3.php', '<?php function testFilesAutoloadGeneration3() {}');
+        file_put_contents($this->vendorDir.'/c/c/foo/bar/test4.php', '<?php function testFilesAutoloadGeneration4() {}');
         file_put_contents($this->workingDir.'/root.php', '<?php function testFilesAutoloadGenerationRoot() {}');
 
         $this->generator->dump($this->config, $this->repository, $package, $this->im, 'composer', false, 'FilesAutoload');
@@ -338,6 +345,8 @@ class AutoloadGeneratorTest extends TestCase
         include $this->vendorDir . '/autoload.php';
         $this->assertTrue(function_exists('testFilesAutoloadGeneration1'));
         $this->assertTrue(function_exists('testFilesAutoloadGeneration2'));
+        $this->assertTrue(function_exists('testFilesAutoloadGeneration3'));
+        $this->assertTrue(function_exists('testFilesAutoloadGeneration4'));
         $this->assertTrue(function_exists('testFilesAutoloadGenerationRoot'));
     }
 
diff --git a/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions.php b/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions.php
index 2c75be906..6080089ec 100644
--- a/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions.php
+++ b/tests/Composer/Test/Autoload/Fixtures/autoload_real_functions.php
@@ -40,7 +40,9 @@ class ComposerAutoloaderInitFilesAutoload
 
         require $vendorDir . '/a/a/test.php';
         require $vendorDir . '/b/b/test2.php';
+        require $vendorDir . '/c/c/foo/bar/test3.php';
         require $baseDir . '/root.php';
+        require $vendorDir . '/c/c/foo/bar/test4.php';
 
         return $loader;
     }