The aims of this study were to evaluate the dental arch relationship (degree of malocclusion) of Japanese patients with unilateral cleft lip and palate (UCLP) at Hokkaido University Hospital and to assess the various congenital and environmental factors that affect dental arch relationship in UCLP patients. Dental models of 140 subjects with UCLP were taken before orthodontic treatment. The mean age of the subjects was 6.85 ± 1.56 (mean ± S.D.) years. Surgeons from Hokkaido University Hospital performed the primary surgery. The dental arch relationships of the 140 subjects were assessed by applying the 5-year-old index and the Goslon Yardstick. The intra- and interexaminer agreement was evaluated using weighted kappa statistics. Associations between various factors and dental arch relationships were assessed using logistic regression analysis. Sixty-nine percent and 79% of the subjects were classified into favorable group (category rating 1, 2 and 3) using the 5-year-old index and the Goslon Yardstick, respectively. Using crude and stepwise regression analyses, significant associations were found between palatoplasty with exposed raw surface and dental arch relationship (judged by the Goslon Yardstick). Family history of skeletal Class III also seemed to be correlated with the dental arch relationship. This multivariate analysis suggested that palatoplasty with exposed raw surface was significantly correlated with the dental arch relationship of UCLP patients at Hokkaido University Hospital. © 2008 Elsevier Ltd and the Japanese Orthodontic Society.