Insulin resistance (IR) and visceral white adipose tissue (WAT) accumulation are the most important pathogenic factors in the development of the metabolic syndrome. WAT plays a central role in the above mentioned disorders both as an insulin sensitive energy-storage tissue and as an endocrine organ. Nowadays, the development of safe and effective drugs for counteracting IR and adiposity is a major medical priority. 3,5-diiodo-L-thyronine (T2), when administered to high fat diet (HFD)-fed rats, prevents body adiposity and IR without inducing deleterious side effects. Here, we investigated the in vivo effects of 4-weeks administration of T2 to HFD rats on WAT phenotype with a particular focus on total tissue protein profile and function by means of two-dimensional gel electrophoresis (2D-E), mass spectrometry (MALDI-TOF and nLC-ESI-MS/MS). T2 profoundly modulates total WAT protein expression profile. Indeed, 30% of total identifiable WAT proteins were significantly (P <0.05) affected by T2-treatment (vs HFD). Of these, 84% were regulated reaching expression levels not differing from those observed in WAT of control (N) animals and 89% were down regulated vs. HFD. Identification by MS of differentially expressed proteins (HFD+T2 vs HFD) and IPA analysis revealed that T2, without inducing thyrotoxicity, positively affects visceral adiposity under an HFD regimen promoting WAT metabolic/proteome reprogramming able to counteract several HFD-induced dysregulations.