To determine whether glycine transporter polymorphisms are associated with alcoholism, three genetic variants of SLC6A5 and two polymorphisms of SLC6A9 were genotyped in 463 German non-alcoholic controls and 644 German alcohol-dependent subjects. Association was investigated employing chi-square statistics and haplotype analysis. There was a significant association between the SLC6A5 polymorphism (rs1443547) and alcohol dependence as alcoholic individuals had a lower rate of AG-allele (chi(2) = 6.048, P = 0.049, d.f. = 2), which did not remain significant after correction for multiple testing. There was no association between SLC6A9 glycine transporter polymorphisms and alcohol dependence, and also none in haplotype analysis.