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As far as I recall, WebLogic cleans up all of its JMS connection pools upon a normal shutdown. This covers connections maintained by resource-reference pools (for application JMS calls), MDBs (for inbound messaging), and bridges (for messaging forwarding). Perhaps your application is caching connections external to these services? If so, then the app needs to be changed so that it closes any of its owned connections on shutdown. Also, MQ itself should be able to automatically clean-up any of it's dead connections - I'm not familiar with MQ tuning, but assume it should have a way to tune this; that said, there may be some limit as to how aggressive you can get with this tuning.