In the present study, we identified the interscapular brown adipose tissue (BAT) genes showing differential expression using DNA microarray analysis in order to better understand a gender-difference in gene regulation, as well as molecular abnormalities in dietinduced obesity. To understand the detailed changes in the gene expression profiles in BAT caused by HFD feeding, we extracted and summarized the genes that were up- or down-regulated by more than 1.5-fold between the genders. In this analysis, significant global changes were observed at the mRNA levels between the genders, as well as lean and obese rat BAT rendered by a HFD. Herein, we report for the first time that a series of genes, which might be involved in fatty acid oxidation and thermogenic regulation, were more highly expressed in females than in males. These results allowed us to conclude that compared to males, females have greater fat clearing capacity through the activation of genes encoding enzymes of fat oxidation. In addition, we found that females have higher thermogenic capacity due to increased expressions of genes involved in energy expenditure. In conclusion, the microarray data of gender dimorphism in BAT will prove valuable in improving gender awareness in the health care system and for the development of evidence-based gender specific clinical recommendations.