A pattern of musculoskeletal impairment inclusive of upper cervical joint dysfunction, combined with restricted cervical motion and impairment in muscle function, has been shown to differentiate cervicogenic headache from migraine and tension-type headache when reported as single headaches. It was questioned whether this pattern of cervical musculoskeletal impairment could discriminate a cervicogenic headache as one type of headache in more complex situations when persons report two or more headaches. Subjects with two or more concurrent frequent intermittent headache types (n = 108) and 57 non-headache control subjects were assessed using a set of physical measures for the cervical musculoskeletal system. Discriminant and cluster analyses revealed that 36 subjects had the pattern of musculoskeletal impairment consistent with cervicogenic headache. Isolated features of physical impairment, e.g. range of movement (cervical extension), were not helpful in differentiating cervicogenic headache. There were no differences in measures of cervical musculoskeletal impairment undertaken in this study between control subjects and those classified with non-cervicogenic headaches.