In order to assess the association of alleles for candidate genes with non-syndromic cleft lip and palate, DNA samples from 43 Japanese patients were compared with those from 73 control subjects with respect to the genes encoding transforming growth factor alpha (TGFalpha), TGFbeta and gamma-aminobutyric acid type A receptor beta3 (GABRB3). The restriction fragment length polymorphisms of the 3'-non-coding region of the TGFalpha gene K-primer region were observed after digestion with NcoI and HinfI. Allele 4 was the most common among cases of cleft lip with or without cleft palate, whereas allele 2 was the most common among controls. A significant difference was found in this region between groups with cleft lip (with or without cleft palate) and controls (chi2=10.190; P=0.017). Three alleles of the TGFbeta2 gene were tested, and allele 2 was the most common in both cases and controls. The proportion of allele 2 in the case group was greater than that in the control group, showing a significant difference between cases of cleft lip (with or without cleft palate) and controls (chi(2)=19.208; P<0.0001). No significant differences in variants of TGFbeta3 or GABRB3 between case and control populations were observed. Thus it is concluded that TGF genes play a role in craniofacial development, and that alleles of TGFalpha or/and TGFbeta2 are associated with cleft lip and cleft palate in Japanese populations.