BACKGROUND Proper understanding of molecular mechanisms underlying gender dimorphism in obesity for better nutritional recommendation is still in early stages. As white adipose tissues (WAT) is most important tissue in obesity metabolism, comparative proteomic analysis of all three WAT deposits at the same time to yield immensely important protein markers was the primary goal of this study. METHODS We performed differential expression analysis of protein profiles of three different WAT viz. subcutaneous, inguinal, and abdominal fat deposits of both genders in lean and obese rats fed a high fat diet (HFD) using a combination of 2-DE and MALDI-TOF-MS. RESULTS The proteomics analysis enabled us to detect 25, 29, and 46 proteins showing gender differences in three WAT deposits, respectively, to gain insight into cause of higher body weight gain in male in response to HFD. CONCLUSIONS The gender dimorphism found in this proteomic study implies that female rats have a lower tendency to undergo metabolic syndrome manifestation, which is associated with lower reliance on lipid as an energy fuel, lower lipogenesis, as well as increased mitochondrial oxidative capacity. In conclusion, most of the candidate proteins identified herein by differential proteomics were previously unrecognized in gender dimorphism of adipose tissue.