diff --git a/src/compiler/commandLineParser.ts b/src/compiler/commandLineParser.ts
index d9f9b040ac6..a8d955d3b16 100644
--- a/src/compiler/commandLineParser.ts
+++ b/src/compiler/commandLineParser.ts
@@ -701,11 +701,11 @@ namespace ts {
                 }
                 else {
                     // by default exclude node_modules, and any specificied output directory
-                    exclude = ["node_modules"];
-                    const outDir = json["compilerOptions"] && json["compilerOptions"]["outDir"];
-                    if (outDir) {
-                        exclude.push(outDir);
-                    }
+                    exclude = ["node_modules", "bower_components", "jspm_packages"];
+                }
+                const outDir = json["compilerOptions"] && json["compilerOptions"]["outDir"];
+                if (outDir) {
+                    exclude.push(outDir);
                 }
                 exclude = map(exclude, normalizeSlashes);
 
diff --git a/tests/cases/unittests/tsconfigParsing.ts b/tests/cases/unittests/tsconfigParsing.ts
index ec025e0b210..776d9495e87 100644
--- a/tests/cases/unittests/tsconfigParsing.ts
+++ b/tests/cases/unittests/tsconfigParsing.ts
@@ -170,5 +170,36 @@ namespace ts {
                 ["/apath/.git/a.ts", "/apath/.b.ts", "/apath/..c.ts"]
             )
         });
+
+        it("always exclude outDir", () => {
+            const tsconfigWithoutExclude =
+            `{
+                "compilerOptions": {
+                    "outDir": "bin"
+                }
+            }`;
+            const tsconfigWithExclude =
+            `{
+                "compilerOptions": {
+                    "outDir": "bin"
+                },
+                "exclude": [ "obj" ]
+            }`;
+            const rootDir = "/";
+            const allFiles = ["/bin/a.ts", "/b.ts"];
+            const expectedFiles = ["/b.ts"];
+            assertParseFileList(tsconfigWithoutExclude, "tsconfig.json", rootDir, allFiles, expectedFiles);
+            assertParseFileList(tsconfigWithExclude, "tsconfig.json", rootDir, allFiles, expectedFiles);
+        })
+
+        it("implicitly exclude common package folders", () => {
+            assertParseFileList(
+                `{}`,
+                "tsconfig.json",
+                "/",
+                ["/node_modules/a.ts", "/bower_components/b.ts", "/jspm_packages/c.ts", "/d.ts", "/folder/e.ts"],
+                ["/d.ts", "/folder/e.ts"]
+            )
+        })
     });
 }