We present seven children with atlantoaxial rotatory fixation (AARF) of more than three months’ duration after an injury to the upper cervical spine. The deformity was irreducible by skull traction. MRI and MR angiography (MRA) of the vertebral arteries were performed in four children. The patients were neurologically intact. Thrombosis of the ipsilateral vertebral artery was noted in two patients. The deformity was gradually corrected and stabilised after transoral release of the atlantoaxial complex, skull traction and posterior atlantoaxial fusion. Soft-tissue interposition and contractures within the atlantoaxial complex prevented closed reduction. MRI and MRA of the vertebral arteries were useful in elucidating the pathology of chronic atlantoaxial rotatory fixation.