Measurement of body composition changes following bariatric surgery is complicated because of the difficulty of measuring body fat in highly obese individuals that have increased photon absorption and are too large for the standard dual-energy X-ray absorptiometry (DXA) table. We reproducibly measured body composition from half-body DXA scans and compared the values of total body fat estimated from total body water (TBW) and DXA measurements before and after Roux-en-Y gastric bypass surgery (RYGB). DXA, TBW (deuterium dilution), extracellular water (ECW; bromide dilution), and intracellular water (ICW) measurement (by subtraction) were made before surgery and at 2 wk, 6 wk, 6 mo, and 12 mo after surgery. Twenty individuals completed baseline and at least four follow-up visits. DXA appeared to underestimate the fat and bone mass in extreme obesity (before surgery), whereas at 6 and 12 mo after surgery, the DXA and TBW fat measurements were similar. The ECW-to-ICW ratio was increased in obese individuals and increased slightly more after surgery. We describe a new model that explains this abnormal water composition in terms of the normal physiological changes that occur in body composition in obesity and weight loss. This model is also used to predict the muscle mass loss following RYGB.