Abstract: A system and method for partial reconfiguration of a gate array includes generating a netlist by placement and routing of a logic circuit. The netlist is accessed to modify logic cells configurations created by the place and route operation. Based on the modifications, a partial configuration bitstream containing only bitstrings which implement the modified logic cells is created. The partial configuration bitstream is downloaded to the gate array, thereby effectuating a partial reconfiguration of the gate array. In an alternate embodiment, a system in accordance with the present invention includes software utilities which allow an application program executing in a system containing a programmable gate array to reconfigure the array on-the-fly. The utilities include routines for modifying the design in response to external conditions detected during run-time. This approach obviates the need for providing a set of predetermined alternate designs, allowing the application to make that determination on its own.