diff --git a/lib/ace/edit_session.js b/lib/ace/edit_session.js
index 3d630ce3..4f31f39a 100644
--- a/lib/ace/edit_session.js
+++ b/lib/ace/edit_session.js
@@ -214,7 +214,7 @@ var EditSession = function(text, mode) {
      *  }
      */
     this.setAnnotations = function(annotations) {
-        this.$annotations = [];
+        this.$annotations = {};
         for (var i=0; i<annotations.length; i++) {
             var annotation = annotations[i];
             var row = annotation.row;
@@ -231,7 +231,7 @@ var EditSession = function(text, mode) {
     };
 
     this.clearAnnotations = function() {
-        this.$annotations = [];
+        this.$annotations = {};
         this._dispatchEvent("changeAnnotation", {});
     };
 
diff --git a/lib/ace/layer/gutter.js b/lib/ace/layer/gutter.js
index a7cd82f1..8088cdbb 100644
--- a/lib/ace/layer/gutter.js
+++ b/lib/ace/layer/gutter.js
@@ -72,12 +72,15 @@ var Gutter = function(parentEl) {
 
     this.setAnnotations = function(annotations) {
         // iterate over sparse array
-        this.$annotations = [];
+        this.$annotations = [];        
         for (var row in annotations) {
+            var rowAnnotations = annotations[row];
+            if (!rowAnnotations)
+                continue;
+                
             var rowInfo = this.$annotations[row] = {
                 text: []
             };
-            var rowAnnotations = annotations[row];
             for (var i=0; i<rowAnnotations.length; i++) {
                 var annotation = rowAnnotations[i];
                 rowInfo.text.push(annotation.text.replace(/"/g, "&quot;").replace(/'/g, "&rsquo;").replace(/</, "&lt;"));