The aim of the present study was to study changes in signs and symptoms of temporomandibular disorders (TMD) and factors predicting TMD signs in adolescents with and without headache. A population-based sample (n = 212) of 13-year-olds with and without headache was re-examined at the age of 16. The study included a questionnaire, face-to-face interview and somatic examination. In addition, a neurological examination, a muscle evaluation and a stomatognathic examination were performed. Significant changes were seen in TMD signs during the follow-up, but TMD signs at the end of the follow-up could not be predicted by baseline headache, sleeping difficulties, depression or muscle pain. TMD signs at the age of 16 were associated with female gender and muscle pain. We conclude that considerable changes in TMD signs occur in the follow-up of adolescents with and without headache. Headache-related TMD are not predictable in adolescents with and without headache.