Abstract This paper reports the development of a comprehensive protective relaying scheme for generator-transformer unit using digital filters. An efficient algorithm based on the recursive constraint transfer function model of the IIR band pass filter has been developed which extracts the various frequency components such as 50, 100, and 150 Hz for realizing the protective functions such as variable bias differential logic, and earth fault protection logic for the combined unit, differential protection logic, rotor over heating relaying logic, reverse power flow relaying logic, rotor earth fault protection logic and field failure relaying logic for the generator, differential protection logic for unit transformer and over fluxing protection logic for the main transformer. In addition to the above relaying functions, the proposed scheme also incorporates a voltage controlled over current relay with IDMT characteristics to give back up for the short-circuit protection for the combined unit. The proposed scheme was tested for different simulated conditions representing normal and abnormal conditions of the system using a PC-80386 computer system. The set limit for discriminating between internal fault and normal condition is considered in terms of the average value rather than RMS value of the three frequency components resulting in reduction of the arithmetical complexity and computational efforts. The proposed scheme as a whole operated satisfactorily by issuing trip signals during internal fault conditions and restraining from tripping during the external fault and normal conditions.