Hardware and software co-synthesis performance estimation includes, for a design specified in a high level programming language and having a processor executable partition and a partition selected for hardware acceleration, estimating hardware latency for a hardware accelerator implementation of the selected partition, scheduling the selected partition using the hardware latency generating hardware partition latency information, and compiling an instrumented version of the design using a processor. The instrumented and compiled version of the design is executed generating software latency information. A design performance for the design is determined through combining the hardware partition latency information with the software latency information.