Purpose To assess and compare the developmental stages and angulations of third molars between the class II and class I sides in class II subdivision malocclusions. Methods This retrospective study was performed using panoramic x-rays of 38 individuals (mean age: 15.5 years; 24 females, 14 males) with class II subdivision malocclusions, which were further divided into type 1 and 2 subgroups according to midline deviation, and a control group of 42 individuals (mean age: 17.0 years; 30 females, 12 males) with normal occlusion. Third molars were categorized using the developmental stages defined by the Demirjian method. Angles between the third molars and horizontal reference lines and also to the second molars were measured. Results No difference was found in developmental stages or angulations between the left and right third molars in the control group. In the class II subdivision malocclusion cases, no difference in third molar developmental stages was observed, but the angle between the long axes of the mandibular third and second molars was significantly greater on the class II side. In the type 2 subgroup, developmental stage of the maxillary third molar was more advanced on the class II side. In both subgroups, the angles of the maxillary third molars' long axis to the interorbital plane differed significantly between the two sides. Conclusion Class II subdivision malocclusion may cause differences in third molar development and angulations between the two sides. Orthodontic treatment should be planned considering the third molars in this malocclusion.