Non-syndromic cleft lip and palate(NSCLP) is one of the most common congenital malformations in human, which is composed of two entities: Cleft lip with or without cleft lip and palate and cleft palate only. NSCLP is a complex disease caused by genetic and environmental factors and their interactions. So far, many candidate genes have been found to be related to this disease, such as interferon regulatory factor 6, methylenetetrahydrofolate reductase, transforming growth factorα, muscle segment homeobox gene 1, retinoic acid receptor α, etc. This review will briefly summarize the relation between most valuable candidate gene site in chromosomes and NSCLP.