An improved electronic design automation (EDA) system employs field programmable gate arrays (FPGAs) for emulating prototype circuit designs. A circuit netlist file is down-loaded to the FPGAs to configure the FPGAs to emulate a functional representation of the prototype circuit. To check whether the circuit netlist is implemented properly, the FPGAs are tested functionally by applying input vectors thereto and comparing the resulting output of the FPGAs to output vectors provided from prior simulation. If the FPGAs fail such vector comparison, the FPGAs are debugged by inserting "read-back" trigger instructions in the input vectors, preferably corresponding to fail points in the applied vector stream. Modifying the input vectors with such read-back signals causes the internal states of latches and flip-flops in each FPGA to be captured when functional testing is repeated. Such internal state information is useful for debugging the FPGAs, and particularly convenient because no recompilation of the circuit netlist is required. A similar approach which also uses the read-back feature of FPGAs is employed to debug FPGAs coupled to a target system which appears to fail during emulation runs.