Functional tolerancing must ensure the assembly and the functioning of a mechanism. This paper compares two methods of tolerance analysis of a mechanical system: the method of “analysis lines” and the method of “polytopes.” The first method needs a discretization of the ending functional surface according to various analysis lines placed on the outer-bound of the face and oriented along the normal of the surface. The second method uses polytopes. The polytopes are defined from the acceptable limits of the geometric deviations of parts and possible displacements between two parts. Minkowski sums and intersections polytopes are then carried out to take into account all geometric variations of a mechanism.