diff --git a/README.md b/README.md
index 402a9565..48fb2769 100644
--- a/README.md
+++ b/README.md
@@ -232,6 +232,7 @@ minimize a global energy function, which is equivalent to statistical multi-dime
 ## v0.4.0 (December 19, 2014)
 Add support for JSX (React) and additional module paths (Thanks to Ben Lowery).
 Fix for detecting presence of AMD or CommonJS modules (Thanks to Aaron Russ).
+Now resolves the module IDs from the RequireJS paths-config properly (Thanks to russaa).
 Added support for option findNestedDependencies to find nested dependencies in AMD modules.
 
 ## v0.3.5 (Septemper 22, 2014)
diff --git a/lib/madge.js b/lib/madge.js
index 11e3b47a..912fae0e 100644
--- a/lib/madge.js
+++ b/lib/madge.js
@@ -28,16 +28,63 @@ function mergeTrees(a, b) {
 		});
 	});
 }
+
 /**
-* Replace alias found inside tree with alias
-* @param  {Object} tree
-* @param  {Object} alias list
-*/
-function convertAliases(tree, aliases) {
-	Object.keys(tree).forEach(function (id) {
-		tree[id].forEach(function (moduleName, i, array) {
-			if (aliases[moduleName]) {
-				array[i] = aliases[moduleName];
+ * Helper for re-mapping path-refs to id-refs that are specified in RequireJS' path config.
+ * @param {Object} deps (dependency-list)
+ * @param {Object} pathDefs (path-definitions from requirejs-config)
+ * @param {String} baseDir (base directory of source files)
+ */
+function convertPathsToIds(deps, pathDefs, baseDir) {
+	var path, pathDeps, i1, len1, i2, len2, isContained;
+
+	if (baseDir){
+		baseDir += '/';
+	} else {
+		baseDir  = '';
+	}
+
+	Object.keys(pathDefs).forEach(function (id) {
+		path = pathDefs[id];
+
+		//if path does not start with / or a protocol: prepend with baseDir
+		if (!/^[^\/]+:\/\/|^\//m.test(path) ){
+			path = baseDir + path;
+		}
+
+		if (path !== id && deps[path]) {
+			if (deps[id] && deps[id].length > 0){
+				pathDeps = deps[path].slice(0, deps[path].length-1);
+
+				//remove entries from <path-ref>, if already contained in <id-ref>
+				for (i1=0, len1 = pathDeps.length; i1 < len1; ++i1){
+					for (i2=0, len2 = deps[id].length; i2 < len2; ++i2){
+						if (pathDeps[i1] === deps[id][i2]){
+							pathDeps.splice(i1--, 1);
+							break;
+						}
+					}
+				}
+				deps[id] = deps[id].concat(pathDeps);
+			} else {
+				deps[id] = deps[path];
+			}
+
+			delete deps[path];
+		} else if (!deps[id]) {
+			deps[id] = [];
+		}
+
+		//normalize entries within deps-arrays (i.e. replace path-refs with id-refs)
+		Object.keys(pathDefs).forEach(function (id) {
+			path = baseDir + pathDefs[id];
+			if (deps[id]){
+				for (i1=0, len1 = deps[id].length; i1 < len1; ++i1){
+					//replace path-ref with id-ref (if necessary)
+					if (deps[id][i1] === path){
+						deps[id][i1] = id;
+					}
+				}
 			}
 		});
 	});
@@ -87,8 +134,10 @@ function Madge(src, opts) {
 	}
 
 	if (this.opts.requireConfig) {
+		var baseDir = src.length ? src[0].replace(/\\/g, '/') : '';
+		baseDir = requirejs.getBaseUrlFromConfig(this.opts.requireConfig, baseDir);
+		convertPathsToIds(tree, requirejs.getPathsFromConfig(this.opts.requireConfig, this.opts.exclude), baseDir);
 		mergeTrees(tree, requirejs.getShimDepsFromConfig(this.opts.requireConfig, this.opts.exclude));
-		convertAliases(tree, requirejs.getPathsFromConfig(this.opts.requireConfig, this.opts.exclude));
 	}
 
 	this.tree = tree;
diff --git a/lib/requirejs.js b/lib/requirejs.js
index 5500b828..f55496b2 100644
--- a/lib/requirejs.js
+++ b/lib/requirejs.js
@@ -4,12 +4,14 @@
  * Module dependencies.
  */
 var fs = require('fs'),
-	parse = require('./parse/parse');
+	parse = require('./parse/parse'),
+	path = require('path');
 
 /**
  * Read shim dependencies from RequireJS config.
  * @param  {String} filename
  * @param  {String} [exclude]
+ * @return {Object}
  */
 module.exports.getShimDepsFromConfig = function (filename, exclude) {
 	var deps = {},
@@ -36,6 +38,7 @@ module.exports.getShimDepsFromConfig = function (filename, exclude) {
 * Read path definitions from RequireJS config.
 * @param  {String} filename
 * @param  {String} [exclude]
+* @return {Object}
 */
 module.exports.getPathsFromConfig = function (filename, exclude) {
 	var paths = {},
@@ -53,3 +56,13 @@ module.exports.getPathsFromConfig = function (filename, exclude) {
 
 	return paths;
 };
+
+/**
+ * Read baseUrl from RequireJS config.
+ * @param  {String} filename
+ * @param  {String} srcBaseDir
+ */
+module.exports.getBaseUrlFromConfig = function (filename, srcBaseDir) {
+	var config = parse.findConfig(filename, fs.readFileSync(filename, 'utf8'));
+	return config.baseUrl ? path.relative(srcBaseDir, config.baseUrl) : '';
+};
\ No newline at end of file
diff --git a/test/amd.js b/test/amd.js
index 84bfb5a1..f52fb4ef 100644
--- a/test/amd.js
+++ b/test/amd.js
@@ -35,7 +35,7 @@ describe('module format (AMD)', function () {
 		madge([__dirname + '/files/amd/requirejs/a.js'], {
 			format: 'amd',
 			requireConfig: __dirname + '/files/amd/requirejs/config.js'
-		}).obj().should.eql({ a: [ 'vendor/jquery-2.0.3' ], 'jquery': [], 'jquery.foo': [ 'vendor/jquery-2.0.3' ], 'jquery.bar': [ 'vendor/jquery-2.0.3' ], 'baz': [ 'vendor/quux' ], 'quux': [] });
+		}).obj().should.eql({ 'a': [ 'jquery' ], 'jquery': [], 'jquery.foo': [ 'jquery' ], 'jquery.bar': [ 'jquery' ], 'baz': [ 'quux' ], 'quux': [] });
 	});
 
 	it('should be able to exclude modules', function () {
@@ -53,7 +53,7 @@ describe('module format (AMD)', function () {
 			format: 'amd',
 			requireConfig: __dirname + '/files/amd/requirejs/config.js',
 			exclude: '^jquery.foo|quux$'
-		}).obj().should.eql({ a: [ 'vendor/jquery-2.0.3' ], 'jquery': [], 'jquery.bar': [ 'vendor/jquery-2.0.3' ] , 'baz': []});
+		}).obj().should.eql({ a: [ 'jquery' ], 'jquery': [], 'jquery.bar': [ 'jquery' ] , 'baz': []});
 	});
 
 	it('should tackle errors in files', function () {
@@ -62,12 +62,6 @@ describe('module format (AMD)', function () {
 		}).obj().should.eql({ error: [] });
 	});
 
-	// it('should handle id different than file', function () {
-	// 	madge([__dirname + '/files/amd/namedWrapped/diff.js'], {
-	// 		format: 'amd'
-	// 	}).obj().should.eql({ 'ffid': [] });
-	// });
-
 	it('should handle named modules', function () {
 		madge([__dirname + '/files/amd/namedWrapped/car.js'], {
 			format: 'amd'
@@ -90,7 +84,7 @@ describe('module format (AMD)', function () {
 		madge([__dirname + '/files/amd/circularAlias'], {
 			format: 'amd',
 			requireConfig: __dirname + '/files/amd/circularAlias/config.js'
-		}).circular().getArray().should.eql([ [ 'dos', 'x86' ] ]);
+		}).circular().getArray().should.eql([ [ 'cpu', 'jsdos' ] ]);
 	});
 
 	it('should find modules that depends on another', function () {