Ligamentous calcification of the cervical spine has been reported in the yellow ligament, anterior and posterior longitudinal ligaments and interspinous ligament. Calcification in the upper cervical spine is rare, although some cases with calcification of the transverse ligament of the atlas have been reported. Two patients with calcification of the alar ligament with an unusual clinical presentation and course are described. Examination by tomography and computed tomography (CT) showed calcification of the alar ligament and the transverse ligament of the atlas. CT documented decreased calcification as symptoms resolved. There may be a role for CT in the search for calcifications in the upper cervical spine in patients presenting with neck pain and pharyngodynia if radiographs are normal.