Cleft lip and/or palate (CL/P) is a major congenital defect with complex etiology, including multiple genetic and environmental factors. Approximately two thirds of the cases are not accompanied by other anomalies and are called nonsyndromic (NS). In the present study, we performed transmission distortion analysis of the MSX1-CA, TGFB3-CA and MTHFR-C677T polymorphisms in 60 parent-child triads, in which the NS-CL/P affected child had at least one affected parent. No association with genes MSX1 or TGFB3 was found, but the results were suggestive of an association of the MTHFR-C677T polymorphism with NS-CL/P. Nonsyndromic cleft lip and/or palate (NS-CL/P) affect about 1/700 livebirths, with wide variability concerning geographic distribution, ethnic background and socioeconomic status (Murray, 2002). The etiology is complex, including multiple genetic and environmental factors. The MSX1 and TGFB3 genes have been suggested as candidate genes based on animal models (Satokata and Maas, 1994;Kaartinen et al., 1995;Proetzel et al., 1995) and association studies in humans with genes MSX1, TGFB3 and MTHFR have pointed to the involvement of these genes in NS-CL/P etiology (Maestri et al., 1997;Lidral et al., 1998;Romitti et al., 1999;Mills et al., 1999; Wyszynsky and Diehl, 2000;Beaty et al., 2001). The MSX1 gene maps to chromosome 4p16. Animal models indicate that this gene plays a role in craniofacial anomalies, leading to a clefting phenotype. Van den Boogaard et al. (2000) identified a stop codon in the MSX1 gene in a three-generation Dutch family with tooth agenesis and combinations of CP only and CLP, providing further evidence for the involvement of this gene in orofacial clefting. Jezewski et al. (2003) sequenced the whole MSX1 gene in a large sample of NS-CL/P patients from different geographic regions, and found mutations in about 2% of the cases.The TGFB3 gene maps to 14q24. Animal model studies demonstrated that TGFB3 plays a role in CP (Kaartinen et al., 1995;1997;Proetzel et al., 1995; Sanford et al., 1997), andLidral et al. (1998) showed an association between TGFB3 markers and NS-CP.The MTHFR gene maps to 1p36.1, and plays a key role in the metabolism of folate by reducing methylenetrahydrofolate to 5-methyltetrahydrofolate, the primary methyl donor for methionine synthesis. The C677T nucleotide variant in the MTHFR gene results in a thermally unstable protein with reduced activity, leading to elevated plasma homocysteine levels. Considerable heterogeneity in the prevalence of the C677T polymorphism throughout the world was reported (Pepe et al., 1998).The present work aimed to investigate if genes TGFB3, MSX1 and MTHFR-C677T are involved in the etiology of NS-CLP, by testing 60 patients, all with an affected parent. We utilized a nuclear family-based approach, to determine for each form of clefting whether these genes were in linkage disequilibrium, as measured by transmission distortion.A total of 60 triads, each one including an affected child and at least one affected parent, were studied. Of...