Background Cleft lip (CL) and cleft palate (CP) are two of the most frequent congenital malformations.Many epidemiologic studies on this deformity have been conducted worldwide, often producing inconsistent results. This study assessed epidemiology and some genetic aspects of cleft lip and palate in a Chinese sample from the Smile Train Program and to compare with other methodologically sound surveys.Methods The general information, family history, classification of cleft and associated malformations of 8000CL and CP surgery patients were analyzed.Results Of the 8000 cases, 7812 had complete data. The distribution of cleft types is 17.04% with CP, 23.39%with CL and 59.58% with cleft lip and palate (CLP). Unilateral clefts were more common than bilateral, with involved 29 CP cases, 41 CL and 156 CLP. The frequency of associated malformations in CLP (3.35%) was higher than CL (2.24%) and CP (2.22%) (P＜0.05). Patients with CP or CLP were born less often in the winter than in the summer (P＜0.05). A history of family members having clefts occurred in 6.84% of patients. The proportion of CLP cases (7.56%) was significantly higher than that of CL cases (5.64%) (P＜0.05).Conclusions The different types of clefts appeared in the highest proportion in CLP and lowest proportion in CP. Males are more common with CL and CLP and less common with CP. These characteristics are the same as those of other Chinese surveys but different from some European reports.