Background: Balkan endemic nephropathy (BEN) is a non-inflammatory, chronic, slow progressing kidney disease, frequently associated with urinary tract tumors. BEN displays familial clustering without an apparent Mendelian inheritance pattern. It has been suggested that environmental toxicants damage urothelial cells in genetically susceptible individuals, which could be the cause of BEN. The metabolism of some substrates that are mediated by glutathione S-transferases (GST), which are polymorphic enzymes, results in nephrotoxic products. To evaluate whether GST genetic heterogeneity could be involved in BEN, we launched a case-control study concerning the association of the most common polymorphic GST variants with BEN.Methods: DNA was extracted from venous blood samples from 54 unrelated BEN patients and 104 controls inhabiting the same endemic region. GSTM1 and GSTT1 null deletions were identified simultaneously by a triplex polymerase chain reaction (PCR) procedure, and GSTP1 polymorphism was analyzed by PCR-restriction fragment length polymorphism (PCR-RFLP) using Alw261.Results: Carriers of at least one GSTM1 wild type allele (wt-allele) were more prevalent among BEN patients compared to controls (chi2=7.92, p=0.005). The GSTT1 and GSTP1 genotype distributions did not demonstrate statistically significant differences between the groups. The carriers of at least one GSTM1 wt-allele among BEN patients were more prevalent in comparison with controls when the GSTM1 genotypes were combined in pairs with all GSTT1 (chi2=9.52, p=0.023) and GSTP1 (chi2=11.92, p=0.036) genotypes. The combined genotype distributions of the three GST genes studied among BEN patients and controls showed that the frequency of carriers of at least one GSTM1 wt-allele among BEN patients was higher or at least equal to the corresponding frequency among controls in all triple combinations. However, this difference did not reach statistical significance (chi2=14.06, p=0.170).Conclusions: GSTM1 wt-allele associates with BEN. The significantly lower prevalence of the GSTM1 deletion homozygotes among BEN patients suggests that individuals bearing the GSTM1 null genotype could be better protected.