The relationship between orthodontic treatment and symptoms and signs of temporomandibular disorders (TMD) was studied prospectively and longitudinally in 65 adolescent girls with Class II malocclusion. The subjects received orthodontic fixed appliance treatment with the straight-wire technique combined with or without extractions and were examined for symptoms and signs of TMD before, during, after, and finally one year post-treatment. Both symptoms and signs of TMD showed considerable fluctuations over the three-year period within the individuals. The general tendency was a decreased prevalence of symptoms of TMD over the three years. The prevalence of pain on mandibular movement and tenderness to palpation of the masticatory muscles was significantly less common during and after orthodontic treatment than before. Clinically registered TMJ clicking increased slightly over the three year period. One orthodontic treatment effect when normalizing Class II malocclusions with fixed appliances was a decreased prevalence of functional occlusal interferences. We concluded that the orthodontic treatment either with or without tooth extractions did not increase the risk for TMD or worsen pre-treatment signs of TMD. Subjects with Class II malocclusion and pre-treatment signs of TMD of muscular origin seemed rather to benefit functionally from orthodontic treatment in a three-year perspective.