Obesity is a leading cause of diabetes mellitus and hypertension. Molecular signals produced by adipose tissue may contribute to the pathogenesis of these two disorders. We have shown previously that a specific segment of rat chromosome 20 (RNO20) contains a gene(s) regulating the degree of obesity, glucose intolerance and hypertension in response to a chronic high-fat diet (HFD). Here, we examined microarray gene-expression profiles and cellular morphology of adipose tissues and whole-body energy expenditure in this model. Adult male spontaneously hypertensive rats (SHR) and a congenic strain (SHR.1N), which differs from SHR by the above-mentioned segment of RNO20, were fed for 12 weeks by HFD or normal diet. At the end of this period, whole-body energy expenditure was measured with indirect calorimetry. In response to HFD, body weight, fat-pad weights, adipocyte size, and serum leptin levels increased significantly more in SHR.1N than SHR. Microarray gene-expression profiles (Affymetrix, 15,923 genes and ESTs) showed that multiple genes of molecular pathways involved in lipogenesis were downregulated to a similar level in both strains, whereas genes involved in fatty acid oxidation and energy dissipation were upregulated less in SHR.1N than SHR. This was associated with lower whole-body energy expenditure in SHR.1N than SHR at the end of the 12-week HFD. Our results suggest that a gene(s) within the RNO20 segment regulate(s) HFD-induced increases in adiposity, and that this effect may be mediated, at least in part, by the impact of that gene(s) on fat burning and energy expenditure.