Aims: To examine whether functional radiography and functional magnetic resonance imaging (MRI) are equal to detect the extent of unstabile anterior atlantoaxial subluxation (aAAS) in rheumatic patients. Methods: The series consisted of 23 patients with unstable aAAS (diagnosed by functional radiography) examined by functional MRI because of a neck symptom. Twenty-two patients had rheumatoid arthritis and one had juvenile idiopathic arthritis. aAAS was diagnosed if the anterior atlanto-axial diameter (AAD) was > 3 mm and was considered unstable if the AAD differed > 2 mm between flexion and extension radiographs. The AAD was measured from radiographs (flexion and extension) and MRI images (flexion and neutral). Results: The extent of aAAS during flexion measured by radiography was greater than that found by MRI in all our 23 cases [the mean difference was 3 mm (95% CI: 2 to 4)]. In 4 patients (17%) MRI could not find aAAS. The difference between the AAD measurements during flexion by these two methods was substantial (i.e. , ≥ 4 mm) in 9 cases (39%). Severe aAAS (≥ 9 mm) was seen in 15 patients (65%) by functional radiography and in 4 (17%) by functional MRI. Conclusions: The magnitude of aAAS was often substantially smaller in functional MRI than in functional radiography. Thus one cannot rely on functional MRI alone; functional radiographs are needed to show the size of unstable aAAS.