In this paper, ‘position and orientation errors of linear and rotary axis average lines’ is newly named ‘geometrical mechanism deviations.’ This paper presents suggestive simulation results of tool motion error caused by geometrical mechanism deviations of a five-axis controlled machine tool. Firstly, there were assumed seven geometrical mechanism deviations consisting of three positional and four angular deviations. As positional deviations, the error of intersection is set to be 0.01 [mm] off-centre, and the squareness errors of the cross axes as angular deviations are 0.01 [°]. Secondly, there was simulated theoretically the shape of machined pyramidal surface according to the virtual cutter movement of a flat end mill along contouring tool paths. Thirdly, the correspondence of geometrical mechanism deviations and simulated flatness error was analysed and found to have two regularities. One of the two indicated that four pyramidal surfaces wave similarly with left half surface up and right half surface down. The other indicated that the centre of a specific pyramidal surface should be concave in the cases of squareness error between B-Z axes. Through the analysis of grouped flatness error, specific geometrical mechanism deviations seem to cause a particular deformation of pyramidal surface due to the misalignment of tool position and orientation.