A messaging system that isolates application programs from the underlying transport and routing mechanisms that are actually used to convey messages. This isolation is provided in part through the use of directory files. The directory files contain all of the specific details (e.g. conversion and routing parameters) necessary to interface with the transport and routing mechanisms. As the transport and routing details change (e.g. due to updated versions or new mechanisms) only the directory files need to be changed. The present invention further includes Message Processing Servers (MPSs) which provide additional messaging functionality such as message storage, tracing, reconciliation, statistical auditing, reformatting, content based routing and multicasting. As additional functionality is developed, this functionality can be flexibly incorporated into a new MPS.