Computed tomography images of 120 dogs were reviewed to characterize variations in atlas morphology, and to identify breed-specific morphologic features. The neural arch of the atlas was thicker in large dogs and male dogs than in small dogs, having a layer of trabecular bone between the inner and outer layers of compact bone. The transverse processes of the atlas were relatively longer in large dogs than in small dogs. Twelve (10%) dogs had incomplete ossification of the atlas. Incomplete ossification of the atlas was associated with gun dogs. Eight dogs had atlantoaxial subluxation. All eight dogs with atlantoaxial subluxation had cervical signs, whereas none of the seven dogs with incomplete ossification of the atlas unaccompanied by atlantoaxial subluxation had clinical signs referable to that area. Of five dogs with both atlantoaxial subluxation and incomplete ossification of the atlas, four had osseous defects affecting both the intercentrum and neural arch, and one had only an osseous defect affecting the neural arch. There was a strong association between incomplete ossification of the atlas and atlantoaxial subluxation (odds ratio 35.0, 95% CI 7.0–175, P=0.00002), which supports the hypothesis that incomplete ossification of the atlas predisposes dogs to atlantoaxial subluxation.