diff --git a/spec/ngdocSpec.js b/spec/ngdocSpec.js
index 187cfac..dcf61f3 100644
--- a/spec/ngdocSpec.js
+++ b/spec/ngdocSpec.js
@@ -293,7 +293,7 @@ describe('ngdoc', function() {
 
 
   describe('checkBrokenLinks', function() {
-    var docs;
+    var docs, apis = {'api': true};
 
     beforeEach(function() {
       spyOn(console, 'log');
@@ -304,7 +304,7 @@ describe('ngdoc', function() {
 
     it('should log warning when a linked page does not exist', function() {
       docs.push(new Doc({section: 'api', id: 'with-broken.link', links: ['non-existing-link']}))
-      ngdoc.checkBrokenLinks(docs);
+      ngdoc.checkBrokenLinks(docs, apis);
       expect(console.log).toHaveBeenCalled();
       var warningMsg = console.log.argsForCall[0][0]
       expect(warningMsg).toContain('WARNING:');
@@ -314,7 +314,7 @@ describe('ngdoc', function() {
 
     it('should log warning when a linked anchor does not exist', function() {
       docs.push(new Doc({section: 'api', id: 'with-broken.link', links: ['api/fake.id1#non-existing']}))
-      ngdoc.checkBrokenLinks(docs);
+      ngdoc.checkBrokenLinks(docs, apis);
       expect(console.log).toHaveBeenCalled();
       var warningMsg = console.log.argsForCall[0][0]
       expect(warningMsg).toContain('WARNING:');
diff --git a/src/ngdoc.js b/src/ngdoc.js
index 06d67c6..ce2c022 100644
--- a/src/ngdoc.js
+++ b/src/ngdoc.js
@@ -1252,18 +1252,21 @@ function merge(docs){
 //////////////////////////////////////////////////////////
 
 
-function checkBrokenLinks(docs) {
+function checkBrokenLinks(docs, apis, options) {
   var byFullId = Object.create(null);
 
   docs.forEach(function(doc) {
     byFullId[doc.section + '/' + doc.id] = doc;
-    if (doc.section === 'api') {
+    if (apis[doc.section]) {
       doc.anchors.push('directive', 'service', 'filter', 'function');
     }
   });
 
   docs.forEach(function(doc) {
     doc.links.forEach(function(link) {
+      if (options && !options.html5mode) {
+        link = link.substring(2);
+      }
       // convert #id to path#id
       if (link[0] == '#') {
         link = doc.section + '/' + doc.id.split('#').shift() + link;
diff --git a/tasks/grunt-ngdocs.js b/tasks/grunt-ngdocs.js
index e08702d..fe1bff0 100644
--- a/tasks/grunt-ngdocs.js
+++ b/tasks/grunt-ngdocs.js
@@ -91,6 +91,7 @@ module.exports = function(grunt) {
     });
 
     ngdoc.merge(reader.docs);
+    ngdoc.checkBrokenLinks(reader.docs, setup.apis, options);
 
     reader.docs.forEach(function(doc){
       // this hack is here because on OSX angular.module and angular.Module map to the same file.