The paper outlines the theoretical background and the calculation method of pallet alignment errors, when palletized components are loaded and unloaded on machining centers. It provides results and the description of a program capable of doing the necessary pallet positioning and orientation error calculations, based on measured data using statistical error analysis. The described method and software can be utilised for machining centers equipped with an Automated Pallet Changer and it can also be integrated into CNC controllers and executed in real-time in computer integrated systems.