Significant differences existed in skeletal morphology between patients with Angle Class II, Division 1 and II, Division 2, with only minor gender-specific differences: angleML/NSL in Class II, Division 2 males (p < 0.01) and females (p < 0.05) was smaller compared to Class II, Division 1 patients. angleML/NL was also noticeably smaller in Class II, Division 2 males (p < 0.001) and females (p < 0.01) compared to Class II, Division 1 patients. Patients with Class II, Division 2 had a smaller gonial angle (angleArGoMe), with the difference being significant only in males (p < 0.05).