Non-syndromic cleft lip with cleft palate (CLP) or without cleft palate (CL), is a common human craniofacial birth defect. CLP and CL are generally very rare in inbred strains of mice, but relatively high frequencies are observed in the “A” strains. We, therefore, chose A/WySn mouse as animal model for our study. Through genetic crosses, 62 N₂ embryos with cleft lip and cleft palate (CLP) and 14 N₂ embryos with cleft lip (CL) were found in 4,340 live implantations. Penetrance analysis indicated that the occurrence of CLP, CL and cleft palate (CP) were influenced by maternal environmental effects during pregnancy. Mapping data indicated candidate genes for CLP on chromosomes 11 (flanked by D11Mit288 and D11Mit334) and 13 (flanked by D13Mit179 and D13Mit159), and candidate genes for CL on chromosomes 13 (flanked by D13Mit179 and D13Mit231) and 9 (flanked by D9Mit24 and D9Mit212) in the A/WySn mouse strain.