CONTEXT: Obesity is a major health problem. Effective treatment requires understanding the homeostatic responses to caloric restriction. OBJECTIVE: The aim was to study Roux-en-Y gastric bypass patients longitudinally for 6 months after surgery to identify major factors modulating fat loss. METHODS: We studied 13 patients (11 females and two males) aged 41.2 ± 2 yr. Mean body mass index was 44.6 ± 1.2 kg/m(2), with 50 ± 1% body fat (58.3 kg). Selection excluded patients with confounding comorbidities or treatments. RESULTS: Caloric intake was reduced 742 ± 82 kcal/d by 1 month and 450 kcal/d between 2 and 4 months postoperatively. By 6 months, relative to baseline, body mass index decreased 24.8 ± 1.1%; percentage body fat, 37.3 ± 3.2% (21.7 kg); fat free mass (FFM), 9.7 ± 1.2%; and resting metabolic rate (RMR), 18.1 ± 4.3%. RMR correlated with FFM at all times (r = 0.71; P < 0.0001), but FFM explained no more than 50% of RMR variance. Exercise capacity (treadmill walking, 53 m/min with increasing grade) improved with time. Mean nonexercise physical activity level was low (1.2, or 20% of RMR), with considerable variance among individuals. Fat loss did not correlate with the aggregate energy deficit or its individual components. Resting or postexercise respiratory exchange ratio (RER) was lowest, whereas plasma β-OH-butyrate and glycerol were highest, between 1 and 2 months after surgery. RER increased linearly with mild exercise, and fat loss correlated positively with physical activity level and RER. CONCLUSIONS: Although the ultimate cause for weight loss is the energy deficit, the variance in fat loss correlated with glucose oxidation, suggesting that glucose partition between oxidation (muscle) and storage (adipose tissue) is an important factor affecting fat loss in individuals submitted to Roux-en-Y gastric bypass.