The objective of this study is to suggest clinical and subclinical atlantoaxial (AA) instability as a cause for dorsal AA ligament hypertrophy responsible for clinical signs in dogs with dens abnormalities. Clinical information from five dogs with malformed dens and dorsal spinal cord compression at the AA junction was collected. All dogs had neck pain, associated with tetraparesis in three cases. Radiological examination revealed hypoplastic dens in two dogs and a defect in its ossification in the other three. Stress views were able to demonstrate obvious AA instability only in two cases, but it was suspected in the other owing to response to surgical fixation of the joint and the presence of a dorsal compressive band, which was considered an enlarged dorsal AA ligament. Surgical and histopathological examination of compressive tissue confirmed hypertrophy of the ligament. Long-term prognosis in the four operated cases, either by dorsal decompression and ventral fixation or by ventral fixation alone, was excellent. A malformed dens can cause subclinical instability, unnoted in dynamic studies. As instability may lead to hypertrophy of joint ligaments, soft tissue changes (specifically dorsal AA ligament hypertrophy) points out this instability and the need for joint fixation if surgical management is required.