Estimating body composition is important to understand the metabolic and cardiovascular effects of adiposity. Estimating changes in body compartments arising from weight loss strategies is equally important to evaluate their benefits and risks, particularly in frail populations (elderly or diabetic), and following bariatric surgery. Body compartments were evaluated in 50 obese subjects (25 diabetic, 25 non-diabetic) before and after a 7 kg weight loss obtained after 6 months of calorie restriction and orlistat. Fat and fat-free mass (FFM) were estimated by bioelectrical impedance analysis (BIA), dual X-ray absorptiometry (DXA), plethysmography (BodPod) and a combination of these in a 3- or 4-compartment model, the latter being considered the reference method. FFM hydration was the ratio of total body water (BIA) to FFM. FFM hydration was significantly higher than classical values (75.9+/-3.0%, P<0.0001), and decreased with weight loss (74.2+/-3.3%). Compared to the 4-compartment, the 3-compartment model gave the most accurate fat and FFM estimation. A significant bias was observed with DXA, BodPod or BIA. Compartment changes induced by weight loss were accurately evaluated by DXA, being particularly precise in the 3-compartment analysis. No effect of diabetes per se was observed. A 3- or 4-compartmental analysis is necessary to accurately estimate body composition and its changes during weight loss.