The server based adapter relies on MQSeries Server running on Microsoft Windows Server. This design of this adapter guarantees reliable messaging because it supports Microsoft Distributed Transaction Coordinator (MSDTC). The adapter supports clustered MQSeries Servers and clustered MQSeries Queue Managers, and also clustered BizTalk servers. For more details about MQSeries Adapter, Please refer this MSDN Page Advantage:
The Client bases adapter is available to connect to Those MQ Servers which are not running on Windows machines. They might be running on UNIX/AIX etc. If there is a requirement to communicate with a MQ server which is running over non windows serves, the solution is use MQSC adapter. In order to use this adapter you would need to install HIS (Host Integration Server) from Microsoft. Refer this dedicated MSDN article about MQ Adapters. Advantage:
The MQSeries adapter uses MSDTC for transactions so it is absolute necessary to check below things before starting:
The following blogs might provide guidance about understanding more about BizTalk and MQ Series:
Another important place to find a huge amount of BizTalk related articles is the TechNet Wiki itself. The best entry point is BizTalk Server Resources on the TechNet Wiki.
Steef-Jan Wiggers edited Revision 7. Comment: Formatting
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I noticed that this was written in 2012, but some of your links, such as MSDN white paper is to BizTalk 2002.
Maheshkumar S Tiwari edited Revision 40. Comment: Minor formatting