The purpose was to analyze skull thickness in incomplete cleft lip (CL), cleft palate (CP), and combined cleft lip and palate (UCLP). Copenhagen School of Dentistry and Copenhagen Cleft Lip and Palate Centre. Patients with cleft lip, cleft palate, and combined cleft lip and palate and normal adult men. Four groups of patients comprised the study. One group of patients with CL (24 patients; 7 women, mean age 6; 17 men, mean age 7.1), one group of patients with UCLP (28 patients; 11 women, mean age 6.6; 17 men, mean age 6.7), one group of patients with CP (57 male patients aged 18-33), and one normal adult male control group. The CL and UCLP groups were compared. The CP group was compared with the normal adult male control group. CL women had a significantly thinner occipital bone compared with CL men (p = 0.027). Women with UCLP had significantly thicker occipital bone than the control women (incomplete CL) (p = 0.014). The study showed gender differences in skull thickness in different cleft types. It also demonstrated that particularly the occipital bone deviated in patients with UCLP, which may explain the considerable deviations in jaw shape and position, previously registered in patients with UCLP.