The Protocol Accelerator is a system which significantly reduces the communication latency of complex layered communication protocols. In particular, the protocol accelerator reduces both the message header overhead imposed by layered protocols and the message processing overhead by employing such techniques as classifying, collecting and aligning the headers, using shorter identifiers to represent information in immutable fields of the headers, introducing pre- and post-processing of a message, packet filtering, and packing and unpacking of messages in cases where a backlog of messages has to be processed by the protocol accelerator.