Deficiency of abTCR+CD4-CD8- (abDN) NKT cells in nonobese diabetic (NOD) mice is a defect that may contribute to susceptibility of the strain to the spontaneous development of Type-1 diabetes. Previously, we mapped genetic control of NKT cell numbers in a backcross from C57BL/6 to the NOD.Nkrp1bmouse strain, in order to elucidate possible genes associated with NKT cell development. An autosomal genome screen revealed significant linkage on chromosomes 1 and 2, and suggestive linkage on chromosomes 7 and 17. Congenic lines were established for the chromosome 1 and 2 linkage regions (NOD. Nkrp1b.Nkt1 b and NOD. Nkrp1b.Nkt2 b) and verified for increased NKT cell numbers. Expression misroarray analyses of NOD mice congenic for these two chromosomal segments identified two interacting peroxisomal integral membrane proteins, suggesting that peroxisomes play a role in NKT cell biology. This was confirmed using a PEX13 conditional knock-out mouse strain. As several of the identified genes are involved in carbon metabolism and are associated with differences in NKT cell numbers and function we tested whether regulation of glycolysis vs oxidative phosphorylation as a source of cellular energy is associated with increased NKT cell numbers. Results of in vitro assays and in vivo pharmaceutical manipulation are consistent with metabolic control of NKT cells being mediated by the predominant source of cellular ATP.