Several skeletal variations of the upper extremity may cause painful conditions or precipitate early degenerative changes, either spontaneously or in response to overuse and trauma. Magnetic resonance imaging has proved particularly useful for accurate interpretation of many of these clinically significant skeletal variations; however, the widespread use of MR imaging may have contributed to over-emphasizing their clinical importance, which is still controversial in many cases. We review, illustrate, and discuss clinically significant skeletal variations of the upper extremity as seen on MR images, particularly those involving the shoulder and the wrist. In the shoulder region, we evaluate variations of acromial and coracoid processes as well as variations and minor dysplastic deformities of the glenoid fossa. We also review different skeletal variations of the carpal region, including ulnar variance, ulnar styloid, lunate morphology, carpal coalition, and carpal accessory ossicles. The role of MR imaging in assessing the clinical importance of such conditions, whether potential, controversial, or well established, is emphasized in this review.