The New Zealand obese (NZO) mouse is a polygenic model of severe obesity and type 2 diabetes-like hyperglycaemia. Outcross experiments with lean strains have led to the identification of numerous susceptibility loci (quantitative trait loci (QTL)) for adiposity and/or hyperglycaemia. Several major QTL were successfully introgressed into lean strains, and two responsible genes, the RabGAP Tbc1d1 and the transcription factor Zfp69, were so far identified by a conventional strategy of positional cloning. Tbc1d1 controls substrate utilization in muscle; SJL mice carry a loss-of-function variant that shifts substrate oxidation from glucose to fat and suppresses adiposity as well as development of diabetes. The zinc finger domain transcription factor Zfp69 appears to regulate triglyceride storage in adipose tissue. Its normal allele Zfp69 causes a redistribution of triglycerides from gonadal stores to liver, and consequently enhances diabetes when introgressed from SJL into NZO, whereas the loss-of-function variant present in NZO and C57BL/6J reduces the prevalence of diabetes. Data from human patients suggest that the orthologs of both genes may play a role in the pathogenesis of the human metabolic syndrome. In addition to Tbc1d1 and Zfp69, variants of Lepr, Pctp, Abcg1, and Nmur2 located in other QTL were identified as potential candidates by sequencing and functional studies. These results indicate that dissection of the genetic basis of obesity and diabetes in mouse models can identify novel regulatory mechanisms that are relevant for the human disease.