This paper describes a method based on an automatic segmentation process to coregister carpal bones of the same patient imaged at different time points. A rigid registration was chosen to avoid artificial bone deformations and to allow finding eventual differences in the bone shape due to erosion, disease regression, or other eventual pathological signs. The actual registration step is performed on the basis of principal inertial axes of each carpal bone volume, as estimated from the inertia matrix. In contrast to already published approaches, the proposed method suggests splitting the 3D rotation into successive rotations about one axis at a time (the so-called basic or elemental rotations). In such a way, singularity and ambiguity drawbacks affecting other classical methods, for instance, the Euler angles method, are addressed. The proposed method was quantitatively evaluated using a set of real magnetic resonance imaging (MRI) sequences acquired at two different times from healthy wrists and by choosing a direct volumetric comparison as a cost function. Both the segmentation and registration steps are not based on a priori models, and they are therefore able to obtain good results even in pathological cases, as proven by the visual evaluation of actual pathological cases.