The paper presents results of analysis how sea waves affect variation of angular speed of a propulsion shaft of the ship during sea passage. That information is necessary to evaluate the level of credibility of measurements taken as reference value for detection of main engine combustion failures and evaluation of cylinders’ contribution to total power based on shaft’s angular speed irregularity observations. Utilization of IAS (Instantaneous Angular Speed) for diagnostic purposes is mostly based on comparison of actual state measurement with characteristics taken during healthy engine run in certain outer conditions. For marine propulsion set, the weather deriving factor, having impact at angular speed of the shaft, is torque variation caused by changes of propeller’s draught due to pitch of the hull. The aim of analysis was to evaluate how pitching frequency affect run of IAS and how to process obtained data to eliminate harmonics deriving from sea waving.