Rationale:In previous studies, few cases of cervical myelopathy caused by invaginated anomalous laminae of the axis have been reported, and none of them was combined with occipitalization of the atlas.Patient concerns:A 28-year-old male was brought to our hospital with motor and sensory impairments of the extremities after a car accident.Diagnoses:MRI showed the spinal cord was markedly compressed at the C2/3 level. Reconstructed CT scans revealed an invaginated laminae of axis into the spinal canal as well as atlas assimilation.Interventions:The patient was successfully managed with surgical treatment by removal of the anomalous osseous structure as well as fixation and fusion.Outcomes:The patient had a rapid recovery after the operation. He regained the normal strength of his 4 extremities and the numbness of his extremities disappeared. He returned to his normal work 3 months after the surgery without any symptoms.Lessons:Invaginated laminae of axis combined with occipitalization of the atlas is a rare deformity. MRI and reconstructed CT scans are useful for both diagnosing and surgical planning of this case. Surgical removal of the laminae results in a satisfactory outcome. The pathogenesis of this anomaly could be the fusion sequence error of the 4 chondrification centers in the embryological term.