diff --git a/src/com/machinepublishers/jbrowserdriver/Context.java b/src/com/machinepublishers/jbrowserdriver/Context.java
index dc034f32a37..d55aabf97ca 100644
--- a/src/com/machinepublishers/jbrowserdriver/Context.java
+++ b/src/com/machinepublishers/jbrowserdriver/Context.java
@@ -92,7 +92,7 @@ void init(final JBrowserDriverServer driver) {
           capabilities.set(new CapabilitiesServer());
           navigation.set(new NavigationServer(
               new AtomicReference<JBrowserDriverServer>(driver), this, statusCode));
-          options.set(new OptionsServer(this, SettingsManager.settings().cookieStore(), timeouts));
+          options.set(new OptionsServer(this, timeouts));
         } catch (RemoteException e) {
           LogsServer.instance().exception(e);
         }
diff --git a/src/com/machinepublishers/jbrowserdriver/CookieStore.java b/src/com/machinepublishers/jbrowserdriver/CookieStore.java
new file mode 100644
index 00000000000..ed20f32bcbe
--- /dev/null
+++ b/src/com/machinepublishers/jbrowserdriver/CookieStore.java
@@ -0,0 +1,157 @@
+/* 
+ * jBrowserDriver (TM)
+ * Copyright (C) 2014-2016 Machine Publishers, LLC
+ * 
+ * Sales and support: ops@machinepublishers.com
+ * Updates: https://github.com/MachinePublishers/jBrowserDriver
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package com.machinepublishers.jbrowserdriver;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.net.CookieHandler;
+import java.net.URI;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.http.cookie.Cookie;
+import org.apache.http.cookie.CookieOrigin;
+import org.apache.http.cookie.CookieSpec;
+import org.apache.http.cookie.MalformedCookieException;
+import org.apache.http.impl.client.BasicCookieStore;
+import org.apache.http.impl.cookie.LaxCookieSpecProvider;
+import org.apache.http.message.BasicHeader;
+
+public class CookieStore extends CookieHandler implements org.apache.http.client.CookieStore, Serializable {
+
+  private static final CookieSpec spec = new LaxCookieSpecProvider().create(null);
+  private final org.apache.http.client.CookieStore store = new BasicCookieStore();
+
+  @Override
+  public Map<String, List<String>> get(URI uri, Map<String, List<String>> requestHeaders) throws IOException {
+    final String reqHost = canonicalHost(uri.getHost());
+    final String reqPath = canonicalPath(uri.getPath());
+    final boolean reqSecure = isSecure(uri.getScheme());
+    final boolean reqJavascript = isJavascript(uri.getScheme());
+    StringBuilder builder = new StringBuilder();
+    if (reqJavascript) {
+      List<Cookie> list;
+      synchronized (store) {
+        store.clearExpired(new Date());
+        list = store.getCookies();
+      }
+      for (Cookie cookie : list) {
+        if ((!cookie.isSecure() || reqSecure)
+            && reqHost.endsWith(canonicalHost(cookie.getDomain()))
+            && reqPath.startsWith(canonicalPath(cookie.getPath()))) {
+          if (builder.length() > 0) {
+            builder.append(';');
+          }
+          builder.append(cookie.getName());
+          builder.append('=');
+          builder.append(cookie.getValue());
+        }
+      }
+    }
+    String cookies = builder.length() == 0 ? null : builder.toString();
+    Map<String, List<String>> map;
+    if (cookies != null) {
+      map = new HashMap<String, List<String>>();
+      map.put("Cookie", Arrays.asList(cookies));
+    } else {
+      map = Collections.emptyMap();
+    }
+    return map;
+  }
+
+  @Override
+  public void put(URI uri, Map<String, List<String>> responseHeaders) throws IOException {
+    if (isJavascript(uri.getScheme())) {
+      for (Map.Entry<String, List<String>> entry : responseHeaders.entrySet()) {
+        for (String value : entry.getValue()) {
+          try {
+            List<Cookie> cookies = spec.parse(new BasicHeader(entry.getKey(), value),
+                new CookieOrigin(uri.getHost(), uri.getPort(), uri.getPath(), isSecure(uri.getScheme())));
+            for (Cookie cookie : cookies) {
+              synchronized (store) {
+                store.addCookie(cookie);
+              }
+            }
+          } catch (MalformedCookieException e) {
+            LogsServer.instance().warn(
+                "Malformed cookie for cookie named " + entry.getKey() + ". " + e.getMessage());
+          }
+        }
+      }
+    }
+  }
+
+  private static boolean isSecure(String scheme) {
+    return "https".equalsIgnoreCase(scheme) || "javascripts".equalsIgnoreCase(scheme);
+  }
+
+  private static boolean isJavascript(String scheme) {
+    return "javascripts".equalsIgnoreCase(scheme) || "javascript".equalsIgnoreCase(scheme);
+  }
+
+  private static String canonicalHost(String host) {
+    if (host == null || host.isEmpty()) {
+      return "";
+    }
+    return host.startsWith(".") ? host.toLowerCase() : "." + host.toLowerCase();
+  }
+
+  private static String canonicalPath(String path) {
+    if (path == null || path.isEmpty()) {
+      return "";
+    }
+    String canonical = path;
+    canonical = canonical.startsWith("/") ? canonical : "/" + canonical;
+    canonical = canonical.endsWith("/") ? canonical : canonical + "/";
+    return canonical.toLowerCase();
+  }
+
+  @Override
+  public void addCookie(Cookie cookie) {
+    synchronized (store) {
+      store.addCookie(cookie);
+    }
+  }
+
+  @Override
+  public List<Cookie> getCookies() {
+    synchronized (store) {
+      return store.getCookies();
+    }
+  }
+
+  @Override
+  public boolean clearExpired(Date date) {
+    synchronized (store) {
+      return store.clearExpired(date);
+    }
+  }
+
+  @Override
+  public void clear() {
+    synchronized (store) {
+      store.clear();
+    }
+  }
+}
diff --git a/src/com/machinepublishers/jbrowserdriver/HttpListener.java b/src/com/machinepublishers/jbrowserdriver/HttpListener.java
index c35fc00606f..1a0c9582147 100644
--- a/src/com/machinepublishers/jbrowserdriver/HttpListener.java
+++ b/src/com/machinepublishers/jbrowserdriver/HttpListener.java
@@ -29,14 +29,8 @@
 import java.util.concurrent.atomic.AtomicLong;
 
 import com.sun.webkit.LoadListenerClient;
-import com.sun.webkit.network.CookieManager;
 
 class HttpListener implements LoadListenerClient {
-  static {
-    //TODO set a cookie manager that extends Java's CookieHandler and implements Apache's CookieStore
-    CookieManager.setDefault(null);
-  }
-
   private static final Map<Integer, String> states;
   private static final Map<Integer, String> errors;
 
diff --git a/src/com/machinepublishers/jbrowserdriver/JBrowserDriverServer.java b/src/com/machinepublishers/jbrowserdriver/JBrowserDriverServer.java
index 3dc48f59399..0cd5c7ac449 100644
--- a/src/com/machinepublishers/jbrowserdriver/JBrowserDriverServer.java
+++ b/src/com/machinepublishers/jbrowserdriver/JBrowserDriverServer.java
@@ -54,6 +54,7 @@
 import com.machinepublishers.jbrowserdriver.Util.Sync;
 import com.sun.javafx.webkit.Accessor;
 import com.sun.webkit.WebPage;
+import com.sun.webkit.network.CookieManager;
 
 import javafx.embed.swing.JFXPanel;
 
@@ -68,6 +69,7 @@ class JBrowserDriverServer extends UnicastRemoteObject implements JBrowserDriver
    * RMI entry point.
    */
   public static void main(String[] args) {
+    CookieManager.setDefault(new CookieStore());
     if (Settings.headless()) {
       System.setProperty("glass.platform", "Monocle");
       System.setProperty("monocle.platform", "Headless");
@@ -165,7 +167,7 @@ public Object perform() {
       }
     });
     Accessor.getPageFor(context.get().item().engine.get()).stop();
-    SettingsManager.settings().cookieStore().clear();
+    ((CookieStore) CookieManager.getDefault()).clear();
     StatusMonitor.instance().clearStatusMonitor();
     LogsServer.instance().clear();
     SettingsManager.register(settings);
diff --git a/src/com/machinepublishers/jbrowserdriver/OptionsServer.java b/src/com/machinepublishers/jbrowserdriver/OptionsServer.java
index 5fbaed0d399..c0d966b72a4 100644
--- a/src/com/machinepublishers/jbrowserdriver/OptionsServer.java
+++ b/src/com/machinepublishers/jbrowserdriver/OptionsServer.java
@@ -27,22 +27,22 @@
 import java.util.Set;
 import java.util.concurrent.atomic.AtomicReference;
 
-import org.apache.http.client.CookieStore;
 import org.apache.http.impl.cookie.BasicClientCookie;
 import org.openqa.selenium.Cookie;
 
+import com.sun.webkit.network.CookieManager;
+
 class OptionsServer extends UnicastRemoteObject implements OptionsRemote,
     org.openqa.selenium.WebDriver.Options {
+  private static final CookieStore cookieStore = (CookieStore) CookieManager.getDefault();
   private final Context context;
   private final ImeHandlerServer imeHandler = new com.machinepublishers.jbrowserdriver.ImeHandlerServer();
-  private final CookieStore cookieStore;
   private final AtomicReference<com.machinepublishers.jbrowserdriver.TimeoutsServer> timeouts;
 
-  OptionsServer(final Context context, final CookieStore cookieStore,
+  OptionsServer(final Context context,
       final AtomicReference<com.machinepublishers.jbrowserdriver.TimeoutsServer> timeouts)
           throws RemoteException {
     this.context = context;
-    this.cookieStore = cookieStore;
     this.timeouts = timeouts;
   }
 
diff --git a/src/com/machinepublishers/jbrowserdriver/Settings.java b/src/com/machinepublishers/jbrowserdriver/Settings.java
index a029fe0f65b..78ddee20f51 100644
--- a/src/com/machinepublishers/jbrowserdriver/Settings.java
+++ b/src/com/machinepublishers/jbrowserdriver/Settings.java
@@ -26,9 +26,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.apache.http.client.CookieStore;
-import org.apache.http.impl.client.BasicCookieStore;
-
 import com.machinepublishers.jbrowserdriver.StreamInjectors.Injector;
 
 /**
@@ -378,7 +375,6 @@ public Settings build() {
   private final boolean saveMedia;
   private final boolean saveAttachments;
   private final String script;
-  private final BasicCookieStore cookieStore;
   private final boolean ignoreDialogs;
   private final boolean cache;
   private final File cacheDir;
@@ -393,7 +389,6 @@ private Settings(Settings.Builder builder) {
     this.proxy = builder.proxy;
     this.saveMedia = builder.saveMedia;
     this.saveAttachments = builder.saveAttachments;
-    this.cookieStore = new BasicCookieStore();
     this.ignoreDialogs = builder.ignoreDialogs;
     this.cache = builder.cache;
     this.cacheDir = builder.cacheDir;
@@ -450,10 +445,6 @@ String script() {
     return script;
   }
 
-  CookieStore cookieStore() {
-    return cookieStore;
-  }
-
   boolean ignoreDialogs() {
     return ignoreDialogs;
   }
diff --git a/src/com/machinepublishers/jbrowserdriver/StreamConnection.java b/src/com/machinepublishers/jbrowserdriver/StreamConnection.java
index 6e947f5defa..4bb26bc4f13 100644
--- a/src/com/machinepublishers/jbrowserdriver/StreamConnection.java
+++ b/src/com/machinepublishers/jbrowserdriver/StreamConnection.java
@@ -102,7 +102,10 @@
 import org.apache.http.ssl.TrustStrategy;
 import org.apache.http.util.EntityUtils;
 
+import com.sun.webkit.network.CookieManager;
+
 class StreamConnection extends HttpURLConnection implements Closeable {
+  private static final CookieStore cookieStore = (CookieStore) CookieManager.getDefault();
   private static final File attachmentsDir;
   private static final File mediaDir;
   private static final File cacheDir;
@@ -469,7 +472,7 @@ public void connect() throws IOException {
               config.get().setProxy(new HttpHost(proxy.host(), proxy.port()));
             }
           }
-          context.get().setCookieStore(SettingsManager.settings().cookieStore());
+          context.get().setCookieStore(cookieStore);
           context.get().setRequestConfig(config.get().build());
           StatusMonitor.instance().addStatusMonitor(url, this);
         }
diff --git a/src/com/machinepublishers/jbrowserdriver/diagnostics/Test.java b/src/com/machinepublishers/jbrowserdriver/diagnostics/Test.java
index d308c9211eb..d5659ccba6d 100644
--- a/src/com/machinepublishers/jbrowserdriver/diagnostics/Test.java
+++ b/src/com/machinepublishers/jbrowserdriver/diagnostics/Test.java
@@ -97,7 +97,7 @@ private Test() {
       test(driver.findElement(By.xpath("//a[contains(@href,'1')]")).getAttribute("id").equals("anchor1"));
 
       /*
-       * Set cookies
+       * Cookie manager
        */
       driver.manage().addCookie(new Cookie("testname", "testvalue"));
       test(driver.manage().getCookieNamed("testname").getValue().equals("testvalue"));
@@ -155,7 +155,14 @@ private Test() {
       test(driver.getCurrentUrl().endsWith("/redirect/site2"));
       test(driver.manage().getCookieNamed("JSESSIONID").getValue().equals("ABC123"));
 
-      //TODO handle cookies set by JS
+      /*
+       * Cookies set by Javascript
+       */
+      test("jsCookieValue1".equals(driver.manage().getCookieNamed("jsCookieName1").getValue()));
+      test("jsCookieValue2".equals(driver.manage().getCookieNamed("jsCookieName2").getValue()));
+      test("jsCookieValue3".equals(driver.manage().getCookieNamed("jsCookieName3").getValue()));
+      test("jsCookieValue4".equals(driver.manage().getCookieNamed("jsCookieName4").getValue()));
+
     } catch (Throwable t) {
       errors.add("Test #" + (curTest + 1) + " -- " + toString(t));
     } finally {
diff --git a/src/com/machinepublishers/jbrowserdriver/diagnostics/iframe.htm b/src/com/machinepublishers/jbrowserdriver/diagnostics/iframe.htm
index 0225e17afb6..fc6c4084ce8 100644
--- a/src/com/machinepublishers/jbrowserdriver/diagnostics/iframe.htm
+++ b/src/com/machinepublishers/jbrowserdriver/diagnostics/iframe.htm
@@ -3,5 +3,9 @@
   </head>
   <body id="iframebody">
     test iframe
+    <script>
+      document.cookie ='jsCookieName3=jsCookieValue3';
+      document.cookie ='jsCookieName4=jsCookieValue4';
+    </script>
   </body>
 </html>
\ No newline at end of file
diff --git a/src/com/machinepublishers/jbrowserdriver/diagnostics/test.htm b/src/com/machinepublishers/jbrowserdriver/diagnostics/test.htm
index d0ffe2f9732..c7ffedcb126 100644
--- a/src/com/machinepublishers/jbrowserdriver/diagnostics/test.htm
+++ b/src/com/machinepublishers/jbrowserdriver/diagnostics/test.htm
@@ -10,7 +10,8 @@
     <span id="testspan"></span>
     
     <script>
-      document.cookie ='cookieName=cookieValue'
+      document.cookie ='jsCookieName1=jsCookieValue1';
+      document.cookie ='jsCookieName2=jsCookieValue2';
     </script>
     <iframe src="iframe.htm" name="testiframe"></iframe>
   </body>