Non-syndromic cleft lip with or without cleft palate (CL/P) is a common birth defect with substantial clinical and social impact and whose causes include both genetic and environmental factors. Folate and homocysteine (Hcy) metabolism have been indicated to play a role in the etiology of CL/P, and polymorphisms in folate and Hcy genes may act as susceptibility factors. We investigated a common polymorphism in the cystathionine beta-synthase (CBS) gene (c.844ins68) in 134 Italian CL/P cases and their parents using the transmission disequilibrium test (TDT). Although no overall linkage disequilibrium was observed, considering the parent-of-origin transmission of the CBS 68 bp insertion a significant (P = 0.002) transmission distortion was detected. When children receive the c.844ins68 allele from the mother compared to the father, they show a 18.7-fold increase in risk for CL/P. This evidence suggests CBS as a candidate gene for CL/P and supports a role of maternal-embryo interactions in the etiology of CL/P.