The position invariant geometric inaccuracies of a machine tool are the first to influence the quality of machined parts. A systematic approach is presented to identify some of these errors on a five-axis machine tool. The methodology is applied to the link error parameters such as joint misalignments, angular offset and rotary axis separation distance. A method based on the mathematical analysis of singularities of linear systems is used to assist in selecting a minimal but sufficient set of link error parameters for the calibration of a machine tool. A number of criteria are proposed in order to verify that the identified parameters accurately predict the positioning errors of the true machine. Finally, the numerical effectiveness of this method is shown through simulations.