Obesity is increasing exponentially in developed countries and constitutes a public health problem by enhancing the risk for metabolic disorder and cardiovascular disease. Differences in gene expression profiles and in metabolic and biochemical properties have been well-described between omental and subcutaneous adipose tissue in humans. Because omental adipose tissue has been strongly associated with the development of insulin resistance, type 2 diabetes and cardiovascular disease, we searched for proteins differentially expressed in these two fat depots using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrometry (MS). In this analysis, we found 43 proteins, several of which were validated by immunoblotting and immunostaining analyses. Results demonstrated tissue-specific molecular differences in the protein makeup of the two analyzed fat depots mainly related to metabolic processes such as glucose and lipid metabolism, lipid transport, protein synthesis, protein folding, response to stress and inflammation. This suggests higher metabolic activity as well as increased cell stress in the omental compared to the subcutaneous fat. These findings provide some insights into the role of omental fat in abdominal obesity-associated co-morbidities.