A system and method for efficient matching regular expression patterns across multiple packets. A deep packet inspection system can be embodied in a switch ASIC using a flow tracker and a signature matching engine. The flow tracker can be positioned in an ingress portion of the switch ASIC at a location where packets in a bi-direction flow can be observed and recorded. The flow tracker generates a signature match request that is forwarded to a signature matching engine in an auxiliary pipeline. The signature matching engine is enabled to perform cross-packet signature matching using signature matching state machines and reports the signature matching results to the flow tracker using a response packet that is sent to the ingress pipeline.