Objective To explore the relationship between nonsyndromic cleft lip with or without cleft palate (NSCL/P) and genetic polymorphism of muscle segment homeobox gene(msx)-1 A448T in Shanxi province population. Methods Case-control study design was employed. msx-1 genotypes were determined by polymerase chain reaction and restriction fragment length polymorphism techniques. Results It was obvious difference between NSCL/P group and control group in msx-1 A448T mutation allele(T) frequency(P0.26). Conclusion We could confirm a significant association between msx-1/A448T polymorphism and NSCL/P in Shanxi province, China. T allele has protective effect in NSCL/P occurrence.