Persistent intermittent headache is a common disorder and is often accompanied by neck aching or stiffness, which could infer a cervical contribution to headache. However, the incidence of cervicogenic headache is estimated to be 14-18% of all chronic headaches, highlighting the need for clear criterion of cervical musculoskeletal impairment to identify cervicogenic headache sufferers who may benefit from treatments such as manual therapy. This study examined the presence of cervical musculoskeletal impairment in 77 subjects, 27 with cervicogenic headache, 25 with migraine with aura and 25 control subjects. Assessments included a photographic measure of posture, range of movement, cervical manual examination, pressure pain thresholds, muscle length, performance in the cranio-cervical flexion test and cervical kinaesthetic sense. The results indicated that when compared to the migraine with aura and control groups who scored similarly in the tests, the cervicogenic headache group had less range of cervical flexion/extension (P=0.048) and significantly higher incidences of painful upper cervical joint dysfunction assessed by manual examination (all P<0.05) and muscle tightness (P<0.05). Sternocleidomastoid normalized EMG values were higher in the latter three stages of the cranio-cervical flexion test although they failed to reach significance. There were no between group differences for other measures. A discriminant analysis revealed that manual examination could discriminate the cervicogenic headache group from the other subjects (migraine with aura and control subjects combined) with an 80% sensitivity.