To investigate overlaps between headache and temporomandibular disorders (TMD) in a clinical headache population and to describe the prevalence of TMD in headache patients, 99 patients referred to a specialized headache centre were diagnosed according to Research Diagnostic Criteria for TMD (RDC/TMD) and classified in headache groups according to the International Classification of Headache Disorders, second edition for headache diagnoses in a blinded design. The prevalence of TMD in the headache population was 56.1%. Psychosocial dysfunction caused by TMD pain was observed in 40.4%. No significant differences in TMD prevalence were revealed between headache groups, although TMD prevalence tended to be higher in patients with combined migraine and tension-type headache. Moderate to severe depression was experienced by 54.5% of patients. Patients with coexistent TMD had a significantly higher prevalence of depression—most markedly in patients with combined migraine and tension-type headache. Our studies indicate that a high proportion of headache patients have significant disability because of ongoing chronic TMD pain. The trend to a higher prevalence of TMD in patients with combined migraine and tension-type headache suggests that this could be a risk factor for TMD development. A need for screening procedures and treatment strategies concerning depression in headache patients with coexistent TMD is underlined by the overrepresentation of depression in this group. Our findings emphasize the importance of examination of the masticatory system in headache sufferers and underline the necessity of a multidimensional approach in chronic headache patients.