diff --git a/lib/network/Network.js b/lib/network/Network.js
index d7528f9a..1df33bdf 100644
--- a/lib/network/Network.js
+++ b/lib/network/Network.js
@@ -247,7 +247,12 @@ Network.prototype.setOptions = function (options) {
 
 
 /**
- * Update the this.body.nodeIndices with the most recent node index list
+ * Update the visible nodes and edges list with the most recent node state.
+ *
+ * Visible nodes are stored in this.body.nodeIndices.
+ * Visible edges are stored in this.body.edgeIndices.
+ * A node or edges is visible if it is not hidden or clustered.
+ *
  * @private
  */
 Network.prototype._updateVisibleIndices = function () {
@@ -258,7 +263,7 @@ Network.prototype._updateVisibleIndices = function () {
 
   for (let nodeId in nodes) {
     if (nodes.hasOwnProperty(nodeId)) {
-      if (nodes[nodeId].options.hidden === false) {
+      if (!this.clustering._isClusteredNode(nodeId) && nodes[nodeId].options.hidden === false) {
         this.body.nodeIndices.push(nodes[nodeId].id);
       }
     }
@@ -266,8 +271,14 @@ Network.prototype._updateVisibleIndices = function () {
 
   for (let edgeId in edges) {
     if (edges.hasOwnProperty(edgeId)) {
-      if (edges[edgeId].options.hidden === false) {
-        this.body.edgeIndices.push(edges[edgeId].id);
+      let edge = edges[edgeId];
+
+      if (!this.clustering._isClusteredEdge(edgeId)
+        && edge.options.hidden === false
+        // Also hidden if any of its connecting nodes are hidden
+        && nodes[edge.fromId].options.hidden === false
+        && nodes[edge.toId  ].options.hidden === false) {
+        this.body.edgeIndices.push(edge.id);
       }
     }
   }
diff --git a/lib/network/modules/Clustering.js b/lib/network/modules/Clustering.js
index f295c162..41692f8f 100644
--- a/lib/network/modules/Clustering.js
+++ b/lib/network/modules/Clustering.js
@@ -5,8 +5,8 @@ var Cluster = require('./components/nodes/Cluster').default;
 class ClusterEngine {
   constructor(body) {
     this.body = body;
-    this.clusteredNodes = {};
-    this.clusteredEdges = {};
+    this.clusteredNodes = {};  // Set of all nodes which are in a cluster
+    this.clusteredEdges = {};  // Set of all edges replaced by a clustering edge
 
     this.options = {};
     this.defaultOptions = {};
@@ -60,14 +60,15 @@ class ClusterEngine {
     let childEdgesObj = {};
 
     // collect the nodes that will be in the cluster
-    for (let i = 0; i < this.body.nodeIndices.length; i++) {
-      let nodeId = this.body.nodeIndices[i];
+    for (let nodeId in this.body.nodes) {
+      if (!this.body.nodes.hasOwnProperty(nodeId)) continue;
+
       let node = this.body.nodes[nodeId];
       let clonedOptions = NetworkUtil.cloneOptions(node);
       if (options.joinCondition(clonedOptions) === true) {
         childNodesObj[nodeId] = this.body.nodes[nodeId];
 
-        // collect the nodes that will be in the cluster
+        // collect the edges that will be in the cluster
         for (let i = 0; i < node.edges.length; i++) {
           let edge = node.edges[i];
           if (this.clusteredEdges[edge.id] === undefined) {
@@ -332,7 +333,7 @@ class ClusterEngine {
 
       // hide the replaced edge
       this._backupEdgeOptions(edge);
-      edge.setOptions({physics:false, hidden:true});
+      edge.setOptions({physics:false});
     }
 
   }
@@ -451,7 +452,7 @@ class ClusterEngine {
           // cache the options before changing
           this._backupEdgeOptions(edge);
           // disable physics and hide the edge
-          edge.setOptions({physics:false, hidden:true});
+          edge.setOptions({physics:false});
         }
       }
     }
@@ -460,7 +461,7 @@ class ClusterEngine {
     for (let nodeId in childNodesObj) {
       if (childNodesObj.hasOwnProperty(nodeId)) {
         this.clusteredNodes[nodeId] = {clusterId:clusterNodeProperties.id, node: this.body.nodes[nodeId]};
-        this.body.nodes[nodeId].setOptions({hidden:true, physics:false});
+        this.body.nodes[nodeId].setOptions({physics:false});
       }
     }
 
@@ -475,14 +476,14 @@ class ClusterEngine {
 
   _backupEdgeOptions(edge) {
     if (this.clusteredEdges[edge.id] === undefined) {
-      this.clusteredEdges[edge.id] = {physics: edge.options.physics, hidden: edge.options.hidden};
+      this.clusteredEdges[edge.id] = {physics: edge.options.physics};
     }
   }
 
   _restoreEdge(edge) {
     let originalOptions = this.clusteredEdges[edge.id];
     if (originalOptions !== undefined) {
-      edge.setOptions({physics: originalOptions.physics, hidden: originalOptions.hidden});
+      edge.setOptions({physics: originalOptions.physics});
       delete this.clusteredEdges[edge.id];
     }
   }
@@ -591,8 +592,7 @@ class ClusterEngine {
         containedNode.vx = clusterNode.vx;
         containedNode.vy = clusterNode.vy;
 
-        // we use these methods to avoid re-instantiating the shape, which happens with setOptions.
-        containedNode.setOptions({hidden:false, physics:true});
+        containedNode.setOptions({physics:true});
 
         delete this.clusteredNodes[nodeId];
       }
@@ -845,6 +845,29 @@ class ClusterEngine {
     return hubThreshold;
   };
 
+
+ /**
+  * Determine if node with given id is part of a cluster.
+  *
+  * @return {boolean} true if part of a cluster.
+  */
+  _isClusteredNode(nodeId) {
+    return this.clusteredNodes[nodeId] !== undefined;
+  }
+
+
+ /**
+  * Determine if edge with given id is not visible due to clustering.
+  *
+  * An edge is considered clustered if:
+  * - it is directly replaced by a clustering edge
+  * - any of its connecting nodes is in a cluster
+  *
+  * @return {boolean} true if part of a cluster.
+  */
+  _isClusteredEdge(edgeId) {
+    return this.clusteredEdges[edgeId] !== undefined;
+  }
 }