This study evaluated the morphological changes in the temporomandibular joint (TMJ) condyles and calculated the Helkimo clinical dysfunction index (CDI) in adolescents with Class II Division 1 malocclusion and mandibular retrognathism treated with the Herbst appliance (phase I) and fixed orthodontic appliances (phase II). Thirty-two consecutive adolescents underwent phase I, and 23 completed phase II. The TMJs were evaluated qualitatively using magnetic resonance imaging (MRI) at the beginning of treatment (T 1 ), during phase I (T 2 ), at the end of phase I (T 3 ) and at the end of phase II (T 4 ). The CDI was calculated at T 1 , T 3 and T 4 . From T 1 to T 3 (p=0.326), there were no changes in condyle morphology in 86.0% of the TMJs. From T 3 to T 4 (p<0.05) and T 1 to T 4 (p<0.05), changes occurred in 39.1% and 43.4% of the condyles. No significant changes in CDI occurred from T 1 to T 3 , T 3 to T 4 and T 1 to T 4 (p=1.000; 86.6%, 76.2% and 76.2% concordance). After phase I, there were practically no changes in condyle morphology. At the end of phase II, a mild flattening was observed in some condyles. It may be concluded that no significant changes occurred in CDI after both treatment phases.