A method and system for modifying the function of a state machine having a programmable logic device. The method includes the steps of modifying a high-level design of the state machine to obtain a modified high-level design of the state machine with a modified function; generating a programmable logic device netlist from differences in the high-level design and the high-level modified design; and installing the modified function into the state machine by programming the programmable logic device based on the programmable logic device netlist.