We present a report of two patients having the association of omovertebra, Sprengel's deformity of the shoulder and Klippel-Feil abnormality with craniovertebral junctional instability. Our literature survey did not locate any report of such association. Significance of bone alterations is analyzed. Two young patients presented with neck pain, torticollis, webbed neck, and spastic quadriparesis. In both patients, the investigations revealed basilar invagination, Klippel-Feil abnormality and Sprengel's deformity of the shoulder. Apart from these relatively common associations, both the patients had omovertebral bone that extended from the transverse process of C5 vertebra to scapula. Following atlantoaxial stabilization surgery, the patients rapidly recovered from all symptoms. Musculoskeletal abnormalities at the craniovertebral junction that include Klippel-Feil abnormality, Sprengel's shoulder, and omovertebra are secondary alterations to primary atlantoaxial instability.