This single-blind comparative group design aimed to investigate the sensitivity and specificity of the cervical flexion-rotation test in the diagnosis of C1/2-related cervicogenic headache. This study tested 23 cervicogenic headache, 23 asymptomatic controls and 12 migraine with aura subjects, all aged 18-66 years. In stage 1, an experienced manipulative physiotherapist who did not partake in the flexion-rotation test procedure identified C1/2 dysfunction using passive segmental mobility tests in the cervicogenic headache group. Those with C1/2 dysfunction participated in stage 2. In stage 2, using the flexion-rotation test, subjects were tested by two experienced manipulative physiotherapists blinded to the subjects' group allocation. Each therapist stated whether the test was positive or not based on the therapist's interpretation of range of motion. The sensitivity and specificity of the flexion-rotation test was 91% and 90%, respectively (P<.001), with an overall diagnostic accuracy of 91% (P<.001). The cervical flexion-rotation test significantly assists in the differential diagnosis of cervicogenic headache and in the identification of movement impairment at the C1/2 segment in patients with cervicogenic headache.