As insulin resistance and NIDDM may both have a genetic basis, we are searching systematically for the involved gene(s) using sib-pair linkage analyses of evenly spaced microsatellite markers in the Pima Indians of the Gila River Indian Community, a population with the highest known prevalence of this disease. We found evidence for linkage and association of insulin resistance and NIDDM with a cluster of microsatellite markers within a 2-3 cM genomic segment at the 7q21.3-q22.1 chromosomal band. In addition, marker D7S479, linked with NIDDM in the Pimas, is also linked with NIDDM in families of Northern European descent living in Utah. Based on these findings we conclude that there is a gene in the region 7q21.3-q22.1 contributing to diabetes susceptibility. Using positional cloning and physical mapping sveral genes were identified in this region. One of these genes, named PDK4, codes for a novel isoform of pyruvate dehydrogenase kinase (PDK). Because of the important role of PDK in the regulation of glucose metabolism, we investigated the PDK4 gene as a possible candidate. However, we found no evidence for any abnormalities in PDK4 that would explain the aboserved linkage of this region with insulin resistance and NIDDM. In addition, we found that the mRNA level of PDK4 (and of a genetically different isoform PDK2) is regulated by insulin, and that insulin-resistant Pima Indians have a higher level of PDK2 and PDK4 mRNA in skeletal muscle. We hypothesize that this observation could reflect a potentially new mechanism contributing to metabolic abnormalities that are characteristic for insulin resistance and NIDDM.