This case-control study evaluated the association of headache and other co-morbid pain with temporomandibular disorder (TMD) pain in adolescents and explored the temporal co-variance of headache and TMD pain. In a population-based sample of 12- to 19-year-olds, 350 patients with self-reported TMD pain and 350 healthy age- and sex-matched individuals were mailed questionnaires. Descriptive statistics, 95% CI, and OR analyses-logistic regression models with TMD pain as the outcome variable and adjusted for age and gender-were used for the analysis of individuals' responses. Headache, whether defined as once a week or more (OR = 6.6) or as moderate or severe (categorical), was significantly related to TMD pain. Severe headache (vs. mild) showed stronger associations with TMD (OR = 10.1) than between moderate and mild headache (OR = 5.5). Neck (OR = 4.0) and back (OR = 2.6) pain was also significantly related to TMD pain. When participants were grouped according to headache onset and TMD pain, the highest association between headache and TMD pain was found in the subgroup "Headache onset before TMD pain" (OR 9.4). In conclusion, headache appears to be independently and highly associated with TMD pain in adolescents. Neck pain and somatic complaints were also significantly associated with TMD pain. Headache seems to precede TMD pain in many adolescents with pain.