A role for allelic variation within the gene for the antioxidant selenoprotein glutathione peroxidase 1 (GPx-1) in the risk or etiology of breast cancer was investigated. By analyzing the frequency of a polymorphism within the GPx-1 gene resulting in a leucine or proline at codon 198, it was determined that the leucine-containing allele was more frequently associated with breast cancer than the proline-containing allele (odds ratio = 1.9; P < 0.05). However, the heterozygosity index for this polymorphism was lower in the breast cancer samples. To determine whether this was because of the loss of heterozygosity (LOH) during tumor development, another polymorphic marker within GPx-1, which is frequently heterozygous in the human population, was analyzed. These studies indicated that LOH at this locus is a frequent event, occurring in approximately 36% of the breast tumor DNAs analyzed. The consequences of the identity of the amino acid at position 198 were investigated by engineering breast carcinoma cells that exclusively express either the leucine- or proline-containing GPx-1 allele and studying the response to increasing concentrations of selenium. These studies indicated that the leucine-containing allele was less responsive to the stimulation of GPx-1 enzyme activity observed during selenium supplementation than the allele differing only by a proline at that position. These studies support a role for GPx-1 allelic identity and LOH as factors of significance to breast cancer development.