The aim of this work is to present a method for the tolerance analysis of an assembly involving free-form surfaces based on dimensional and geometric tolerances. The great effort of the present work is to deal with dimensional and geometric tolerances applied to free-form surfaces. The case of study is the flaperon, a structural component of the aircraft, that is constituted by one skin cover, eight ribs, and one spar. The ten components of the flaperon are connected by adhesive, in order to overcome the problems due to the rivets use. Adhesive thickness between the faced parts to connect should be as constant as possible in order to obtain the right structural connection. The influence of the tolerances applied to the ten components of the flaperon on the value of the gap at the interfaces among each couple of components has been deeply investigated by means of the proposed method. Moreover, the influence of the tolerances on the aerodynamic performances of the flaperon has also been analyzed.