The purpose of this study was to clarify differences in skeletal morphologies between male and female orthodontic patients with and without agenesis of all four third molars. A total of 64 patients (32 males and 32 females) with agenesis of all four third molars without agenesis of other teeth were selected as the third molars agenesis group (group 1). In addition, 64 patients (32 males and 32 females) with all these teeth were selected as controls (group 2). Lateral cephalograms taken between the ages of 14 and 30 years were used to compare skeletal morphology between groups 1 and 2 and between sexes. Maxillary length (P < 0.001), lower facial height (P < 0.05), gonial angle (P < 0.001) and mandibular plane angle (P < 0.001) were significantly smaller in group 1 than in group 2. Irrespective of the presence or absence of all four third molars, males had significantly smaller lower facial height (P < 0.01) and mandibular plane angle (P < 0.001) and significantly greater total mandibular length (P < 0.001), mandibular body length (P < 0.001) and mandibular ramus height (P < 0.001) than females. Japanese orthodontic patients with agenesis of all four third molars had significantly small maxillary length, lower facial height, gonial angle and mandibular plane angle.