diff --git a/jsdoc.js b/jsdoc.js
index bac8f91a..02f28d14 100644
--- a/jsdoc.js
+++ b/jsdoc.js
@@ -245,13 +245,15 @@ function main() {
             env.opts._.splice(i--, 1);
         }
     }
-
+    
+    if (env.opts.source.include) {
+        env.opts._ = (env.opts._ || []).concat(env.opts.source.include);
+    }
+    
     if (env.opts._.length > 0) { // are there any files to scan and parse?
+        var filter = new (require('jsdoc/src/filter').Filter)(env.conf.source);
 
-        var includeMatch = (env.conf.source && env.conf.source.includePattern)? new RegExp(env.conf.source.includePattern) : null,
-            excludeMatch = (env.conf.source && env.conf.source.excludePattern)? new RegExp(env.conf.source.excludePattern) : null;
-
-        sourceFiles = app.jsdoc.scanner.scan(env.opts._, (env.opts.recurse? 10 : undefined), includeMatch, excludeMatch);
+        sourceFiles = app.jsdoc.scanner.scan(env.opts._, (env.opts.recurse? 10 : undefined), filter);
 
         require('jsdoc/src/handlers').attachTo(app.jsdoc.parser);
 
diff --git a/rhino_modules/jsdoc/src/filter.js b/rhino_modules/jsdoc/src/filter.js
new file mode 100644
index 00000000..a2664305
--- /dev/null
+++ b/rhino_modules/jsdoc/src/filter.js
@@ -0,0 +1,43 @@
+/**
+	@module jsdoc/src/filter
+	
+	@author Michael Mathews <micmath@gmail.com>
+	@license Apache License 2.0 - See file 'LICENSE.md' in this project.
+ */
+
+/**
+    @constructor
+    @param {object} opts
+    @param {string[]} opts.exclude - Specific files to exclude.
+    @param {string|RegExp} opts.includePattern
+    @param {string|RegExp} opts.excludePattern
+ */
+exports.Filter = function(opts) {
+    this.exclude = opts.exclude || null;
+    this.includePattern = opts.includePattern? 
+                            typeof opts.includePattern === 'string'? new RegExp(opts.includePattern) : opts.includePattern
+                            : null;
+    this.excludePattern = opts.excludePattern? 
+                            typeof opts.excludePattern === 'string'? new RegExp(opts.excludePattern) : opts.excludePattern
+                            : null;
+}
+
+/**
+    @param {string} filepath - The filepath to check.
+    @returns {boolean} Should the given file be included?
+ */
+exports.Filter.prototype.isIncluded = function(filepath) {
+    if ( this.includePattern && !this.includePattern.test(filepath) ) {
+        return false;
+    }
+    
+    if ( this.excludePattern && this.excludePattern.test(filepath) ) {
+        return false;
+    }
+    
+    if ( this.exclude && this.exclude.indexOf(filepath) > -1 ) {
+        return false;
+    }
+    
+    return true;
+}
\ No newline at end of file
diff --git a/rhino_modules/jsdoc/src/scanner.js b/rhino_modules/jsdoc/src/scanner.js
index 9b8ff7e6..2c5ad30a 100644
--- a/rhino_modules/jsdoc/src/scanner.js
+++ b/rhino_modules/jsdoc/src/scanner.js
@@ -28,7 +28,7 @@ common.mixin(exports.Scanner.prototype, common.events);
 	@param {number} [depth=1]
 	@fires sourceFileFound
  */
-exports.Scanner.prototype.scan = function(searchPaths, depth, includeMatch, excludeMatch) {
+exports.Scanner.prototype.scan = function(searchPaths, depth, filter) {
 	var filePaths = [],
 	    that = this;
 
@@ -45,15 +45,7 @@ exports.Scanner.prototype.scan = function(searchPaths, depth, includeMatch, excl
 	});
 	
 	filePaths = filePaths.filter(function($) {
-	    if (includeMatch && !includeMatch.test($)) {
-	        return false
-	    }
-	    
-	    if (excludeMatch && excludeMatch.test($)) {
-	        return false
-	    }
-	    
-	    return true;
+	    return filter.isIncluded($);
 	});
 	
 	filePaths = filePaths.filter(function($) {
diff --git a/test/specs/jsdoc/src/filter.js b/test/specs/jsdoc/src/filter.js
new file mode 100644
index 00000000..9d744271
--- /dev/null
+++ b/test/specs/jsdoc/src/filter.js
@@ -0,0 +1,19 @@
+describe("jsdoc/src/filter", function() {
+    var filter = new (require('jsdoc/src/filter').Filter)({
+            includePattern: new RegExp(".+\\.js(doc)?$"),
+            excludePattern: new RegExp("(^|\\/)_"),
+            exclude: ['.ignore', 'scratch/conf.js']
+        });
+
+    var files = ['yes.js', '/yes.jsdoc', '/_nope.js', '.ignore'];
+    
+    files = files.filter(function($) {
+        return filter.isIncluded($);
+    });
+
+    it("should return the correct source files", function() {
+        expect(files.length).toEqual(2);
+        expect(files.indexOf("yes.js")).toBeGreaterThan(-1);
+        expect(files.indexOf("/yes.jsdoc")).toBeGreaterThan(-1);
+    });
+});
\ No newline at end of file
diff --git a/test/specs/jsdoc/src/scanner.js b/test/specs/jsdoc/src/scanner.js
index 5b82dffd..e9f127e7 100644
--- a/test/specs/jsdoc/src/scanner.js
+++ b/test/specs/jsdoc/src/scanner.js
@@ -1,8 +1,10 @@
 describe("jsdoc/src/scanner", function() {
     var scanner = new (require('jsdoc/src/scanner').Scanner)(),
-        includeMatch = new RegExp(".+\\.js(doc)?$"),
-        excludeMatch = new RegExp("(^|\\/)_"),
-        sourceFiles = scanner.scan([__dirname+'/test/fixtures/src/'], 3, includeMatch, excludeMatch);
+        filter = new (require('jsdoc/src/filter').Filter)({
+            includePattern: new RegExp(".+\\.js(doc)?$"),
+            excludePattern: new RegExp("(^|\\/)_")
+        }),
+        sourceFiles = scanner.scan([__dirname+'/test/fixtures/src/'], 3, filter);
 
     sourceFiles = sourceFiles.map(function($) {
         return $.replace(__dirname, '');