Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common craniofacial birth defect that is the result of a mixture of genetic and environmental factors. While studies have identified a number of different candidate genes and loci for the etiology of CL/P, the results have not been consistent among different ethnic groups. To study the genetic association of the candidate genes in Korean patients affected by CL/P, we genotyped 97 nonsyndromic CL/P patients and 100 control individuals using single nucleotide polymorphic markers at the MTHFR, TGFA, and IRF6 genes. We report that the T3827C marker at TGFA showed significant association with nonsyndromic CL/P, but all the other markers tested were not significantly associated with nonsyndromic CL/P in Korean patients.