In some cases message can be "lost" while it is processing by pipeline, the reason can be damaged XML format or unexpected error. So you will not be able to find the lost message in Failed Messages (Group Hub) in Event Viewer you will find something like There was a failure executing the receive pipeline: "Microsoft.BizTalk.DefaultPipelines.XMLReceive, Microsoft.BizTalk.DefaultPipelines, Version=3.0.1.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" Source: "XML disassembler" Receive Port: "ReceivePort1" URI: "C:\Temp\rcv\*.txt" Reason: No Disassemble stage components can recognize the data. To solve the problem you should enable routing for failed messages in receive port Then create a send port which will filter all failed messages for you