While debugging, a user chooses an incremental recompile. Internal signals of interest are selected and output pins are optionally reserved. An incremental recompile of the compiled design includes compiling a routing from each internal signal to an output pin. The technology-mapped netlist and placing and routing information corresponding to an original compiled design are saved into a database during full compilation. During debugging, an incremental compiler retrieves this information to build the original routing netlist. The database building, logic synthesis and technology mapping stages may be skipped. New connections are added, fitted to the device, and then the final routing netlist is output into a programming output file (POF) in a form suitable for programming the PLD. The user views the internal signals at the output pins chosen. The user may iterate through this process many times in order to debug the PLD. The debugging assignments may be deleted.