Tap-1 and Tap-2 genes code for a heterodimeric peptide transporter required for the normal maturation and surface expression of class I molecules. Polymorphic variants of these MHC encoded genes occur in rats and humans. After failing to amplify a 3' polymerase chain reaction (PCR) product from thymic and splenic cDNA of the nonobese nondiabetic (NON) strain, we considered it possible that Tap-1 polymorphism was present, since cDNA from CBA/J, C57BL/6, BALB/c, and NOD (nonobese diabetic) mice all yielded Tap-1 3' products. Overlapping PCR fragments spanning the highly conserved ATP-binding cassette (ABC) were generated for purposes of restriction endonuclease analysis, studies of IFN-gamma regulation, and sequencing. To avoid amplifying other members of the transporter family, we used a gel-purified 1670-bp Tap-1 PCR "long product" as template for nested PCR. Sequencing revealed three polymorphic alleles. The most divergent was for the NON strain and involved two non-conserved amino acid substitutions (Arg-->Cys397 and Leu-->Arg491) and three silent mutations. NON mice show an abnormal pattern of class I (Kb) expression and a sizeable reduction in the percentage of CD8+ cells in the blood and thymus. In F2 segregants, the low CD8 phenotype mapped to the MHC. Tap-1 genes of NON and C57BL/6 mice were equally sensitive to up-regulation by IFN-gamma. We conclude that the mouse Tap-1 transporter gene, like the Tap-2 of the rat and the Tap-1 and Tap-2 of the human, is polymorphic. The extensive variation and specific codon changes of Tap-1 in the NON mouse raise the possibility that this gene is the MHC locus responsible for altering the intrathymic development of CD8+ T cells.