OBJECTIVE To analyze gender differences in cleft pattern by the clinical statistical study of Japanese patients with cleft lip and/or cleft palate. METHODS Cleft pattern modeling was used to analyze 782 patients with cleft lip and/or cleft palate (417 males and 365 females) who had been examined at the Cleft Lip and Palate Center, Aichi-Gakuin University Hospital, and whose details could be confirmed. Relationships between gender and cleft type were analyzed with chi-squared test. RESULTS A comparison of gender differences by cleft type revealed that a greater percentage of males had milder cleft lip, cleft lip and palate, or cleft palate, whereas the percentage of females tended to be greater as cleft severity increased. CONCLUSIONS Modeling of cleft patterns enables more detailed classification of cleft lip and palate, and can lead to a greater understanding of pathology.