A method, system, and apparatus for processing messages according to one or more stateful protocols in a data communication system. Messages belonging to various communication flows (such as TCP transport layer “connections”) are processed according to a selected stateful protocol. Messages belonging to a single unified flow are distributed among different protocol processing cores (PPCs) at different times. Assignment of flows to PPCs is typically modifiable at the level of specific individual flows, permitting flexible load balancing between PPCs. The architecture of the system facilitates the method by providing a mix of pipelined and parallel processing structures.