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BACKGROUND Atlantoaxial rotatory dislocation (AARD) in children may be caused by neck trauma or an upper respiratory tract infection. Here the authors describe the very rare association between inflammatory bowel disease and AARD in a child. OBSERVATIONS A 7-year-old girl presented with an 11-month history of torticollis that occurred spontaneously without a trauma context. Her history revealed a recent diagnosis of Crohn’s disease. Physical exam of the cervical spine revealed a “cock-robin” posture. Neck radiography and three-dimensional computed tomography reconstruction established the diagnosis of AARD. Given the duration of the symptoms and failure of previous conservative treatments, the patient was taken to the operating room and underwent open reduction through posterior approach with a C1–2 fusion according to the Harms technique. The torticollis resolved with no recurrence at the last follow-up and minimal restriction of rotation. LESSONS This is the third report to describe the very rare association between inflammatory bowel disease and AARD but at a very early age, the youngest in the literature. One should be aware of such association as early diagnosis may prevent aggressive surgical management.