Methods and circuits in an application circuit to compensate for skew in the transmission of serial data between field programmable gate arrays (FPGAs) in the application circuit. A clock signal source external to both FPGAs generates a clock signal applied to both FPGAs. A transmitting FPGA generates a serial data stream comprising the current values of a plurality of signals within the transmitting FPGA and transmits the serial data stream based on its clock signal. The receiving FPGA receives the serial data stream and applies a programmed delay to the received serial data stream to compensate for skew in received serial data stream relative to its clock signal. The programmed delay value may be determined at initialization (or reset) of the FPGAs by transmitting synchronization data from the first transmitting FPGA to the receiving FPGA. The receiving FPGA adjusts a programmable delay while receiving synchronization data until it sense bit and word alignment relative to its clock signal.