diff --git a/package.json b/package.json
index d878300f45a..b8871aac121 100644
--- a/package.json
+++ b/package.json
@@ -41,6 +41,7 @@
     "commander": "^2.9.0",
     "diff": "^3.2.0",
     "glob": "^7.1.1",
+    "minimatch": "^3.0.4",
     "resolve": "^1.3.2",
     "semver": "^5.3.0",
     "tslib": "^1.7.1",
@@ -57,6 +58,7 @@
     "@types/diff": "^3.2.0",
     "@types/glob": "^5.0.30",
     "@types/js-yaml": "^3.5.29",
+    "@types/minimatch": "^2.0.29",
     "@types/mocha": "^2.2.35",
     "@types/node": "^7.0.16",
     "@types/resolve": "^0.0.4",
diff --git a/src/runner.ts b/src/runner.ts
index f4c44d3be9b..5ae114e9d6b 100644
--- a/src/runner.ts
+++ b/src/runner.ts
@@ -19,6 +19,7 @@
 
 import * as fs from "fs";
 import * as glob from "glob";
+import { Minimatch } from "minimatch";
 import * as path from "path";
 import * as ts from "typescript";
 
@@ -171,9 +172,11 @@ async function runLinter(options: Options, logger: Logger): Promise<LintResult>
 }
 
 function resolveFilesAndProgram({ files, project, exclude, outputAbsolutePaths }: Options): { files: string[]; program?: ts.Program } {
-    // if both files and tsconfig are present, use files
+    // remove single quotes which break matching on Windows when glob is passed in single quotes
+    const ignore = arrayify(exclude).map(trimSingleQuotes);
+
     if (project === undefined) {
-        return { files: resolveFiles() };
+        return { files: resolveGlobs(files, ignore, outputAbsolutePaths) };
     }
 
     const projectPath = findTsconfig(project);
@@ -182,17 +185,21 @@ function resolveFilesAndProgram({ files, project, exclude, outputAbsolutePaths }
     }
 
     const program = Linter.createProgram(projectPath);
-    return { files: files === undefined || files.length === 0 ? Linter.getFileNames(program) : resolveFiles(), program };
-
-    function resolveFiles(): string[] {
-        return resolveGlobs(files, exclude, outputAbsolutePaths === true);
+    let filesFound: string[];
+    if (files === undefined || files.length === 0) {
+        filesFound = Linter.getFileNames(program);
+        if (ignore.length !== 0) {
+            const mm = ignore.map((pattern) => new Minimatch(path.resolve(pattern)));
+            filesFound = filesFound.filter((file) => !mm.some((matcher) => matcher.match(file)));
+        }
+    } else {
+        filesFound = resolveGlobs(files, ignore, outputAbsolutePaths);
     }
+    return { files: filesFound, program };
 }
 
-function resolveGlobs(files: string[] | undefined, exclude: Options["exclude"], outputAbsolutePaths: boolean): string[] {
-    const ignore = arrayify(exclude).map(trimSingleQuotes);
+function resolveGlobs(files: string[] | undefined, ignore: string[], outputAbsolutePaths?: boolean): string[] {
     return flatMap(arrayify(files), (file) =>
-        // remove single quotes which break matching on Windows when glob is passed in single quotes
         glob.sync(trimSingleQuotes(file), { ignore, nodir: true }))
         .map((file) => outputAbsolutePaths ? path.resolve(file) : path.relative(process.cwd(), file));
 }
diff --git a/test/executable/executableTests.ts b/test/executable/executableTests.ts
index f7f890ef993..2ecd8cf9f3c 100644
--- a/test/executable/executableTests.ts
+++ b/test/executable/executableTests.ts
@@ -339,6 +339,15 @@ describe("Executable", function(this: Mocha.ISuiteCallbackContext) {
                     done();
                 });
         });
+
+        it("works with '--exclude'", (done) => {
+            execCli(
+                [ "-p", "test/files/tsconfig-allow-js/tsconfig.json", "-e", "'test/files/tsconfig-allow-js/testfile.test.js'"],
+                (err) => {
+                    assert.isNull(err, "process should exit without an error");
+                    done();
+                });
+        });
     });
 
     describe("--type-check", () => {
diff --git a/test/files/tsconfig-allow-js/tslint.json b/test/files/tsconfig-allow-js/tslint.json
index 8b3ddc16690..9f90c6f0336 100644
--- a/test/files/tsconfig-allow-js/tslint.json
+++ b/test/files/tsconfig-allow-js/tslint.json
@@ -1,4 +1,10 @@
 {
+    "rules": {
+        "eofline": true,
+        "semicolon": [
+            true, "always"
+        ]
+    },
     "jsRules": {
         "eofline": true,
         "semicolon": [
diff --git a/test/files/tsconfig-allow-js/valid.test.ts b/test/files/tsconfig-allow-js/valid.test.ts
new file mode 100644
index 00000000000..cb0ff5c3b54
--- /dev/null
+++ b/test/files/tsconfig-allow-js/valid.test.ts
@@ -0,0 +1 @@
+export {};
diff --git a/yarn.lock b/yarn.lock
index 7a1cdee20f5..618624a3c14 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -35,7 +35,7 @@
   version "3.5.30"
   resolved "https://registry.yarnpkg.com/@types/js-yaml/-/js-yaml-3.5.30.tgz#f555118c022318e57e36d803379cb8ee38ee20a7"
 
-"@types/minimatch@*":
+"@types/minimatch@*", "@types/minimatch@^2.0.29":
   version "2.0.29"
   resolved "https://registry.yarnpkg.com/@types/minimatch/-/minimatch-2.0.29.tgz#5002e14f75e2d71e564281df0431c8c1b4a2a36a"
 
@@ -1475,7 +1475,7 @@ tslint@latest:
     tslib "^1.6.0"
     tsutils "^2.0.0"
 
-tsutils@2, tsutils@^2.0.0:
+tsutils@^2.0.0, tsutils@^2.3.0:
   version "2.3.0"
   resolved "https://registry.yarnpkg.com/tsutils/-/tsutils-2.3.0.tgz#96e661d7c2363f31adc8992ac67bbe7b7fc175e5"