Obesity and type II diabetes are complex diseases in the human population. The existence of a large number of contributing loci and gene/gene as well as gene/environment interactions make it difficult to identify the disease genes underlying these complex traits. In mouse models of obesity and type II diabetes such as the murine fat mutation, genetic crosses can be used to dissect the genetic complexity influencing the observed phenotypes. The underlying defect in the fat mutant is a Ser202Pro change in carboxypeptidase E (CPE), an enzyme responsible for the final proteolytic processing step of prohormone intermediates. On the HRS/J (HRS) inbred strain background, mice homozygous for the fat mutation exhibit early onset hyperinsulinemia followed by post-pubertal moderate obesity without hyperglycemia. In contrast, on the C57BLKS/J (BKS) genetic background, fat/fat mice become severely obese, hyperinsulinemic, and hyperglycemic. Therefore, in the Cpe^fat genetic model, the fat mutation is necessary, but not sufficient for the development of obesity, type II diabetes and related metabolic disorders. To dissect the susceptibility loci responsible for modifying obesity and diabetes associated traits, we characterized, both genetically and phenotypically, fat/fat male progeny from a large intercross between BKS.HRS-fat/fat and HRS-+/+ mice. Four major loci were mapped including a locus for body weight (bwt1: body weight 1) on chromosome 14, a locus for hyperglycemia (find1: fat-induced diabetes 1) on chromosome 19, a locus for hyperglycemia, hyperinsulinemia, and hypercholesterolemia (find2: fat-induced diabetes 2) on chromosome 5, and a locus for adiposity and body weight (fina1: fat-induced adiposity 1) on chromosome 11. The identification of these interacting genetic determinants for obesity and type II diabetes may allow better definition of the obesity/diabetes related hormone signaling pathways and ultimately may provide new insights into the pathogenesis of these complex diseases.