I am using JMS to communicate between EJBs and client (GUI) classes in my application.

Suresh, I think we'll need a few more details before you can be helped. How is JMS being used here? Are you using queues or pub-sub? What type of payload are in your messages? Have you looked to verify that you don't have some sort of deadlock situation causing your thread to wait forever? How is the communication between the EJBs being done? Is it via JMS or a direct EJB call?