http://stackoverflow.com/questions/8682051/ios-application-how-to-clear-notifications
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Just to expand on pcperini's answer. As he mentions you will need to add the following code to yourapplication:didFinishLaunchingWithOptions: method;
[[UIApplication sharedApplication] setApplicationIconBadgeNumber: 0];
[[UIApplication sharedApplication] cancelAllLocalNotifications];
You Also need to increment then decrement the badge in your application:didReceiveRemoteNotification: method if you are trying to clear the message from the message centre so that when a user enters you app from pressing a notification the message centre will also clear, ie;
[[UIApplication sharedApplication] setApplicationIconBadgeNumber: 1];
[[UIApplication sharedApplication] setApplicationIconBadgeNumber: 0];
[[UIApplication sharedApplication] cancelAllLocalNotifications];
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