Background: Weight loss leads to reduced resting energy expenditure (REE) independent of fat-free mass (FFM) and fat mass (FM) loss, but the effect of changes in FFM composition is unclear. Objective: We hypothesized that a decrease in REE adjusted for FFM with weight loss would be partly explained by a disproportionate loss in the high metabolic activity component of FFM. Design: Forty-five overweight and obese women [body mass index (in kg/m 2 ): 28.7-46.8] aged 22-46 y followed a low-calorie diet for 12.7 6 2.2 wk. Body composition was measured by magnetic resonance imaging, dual-energy X-ray absorptiometry, and a 4-compartment model. REE measured by indirect calorimetry (REEm) was compared with REE calculated from detailed body-composition analysis (REEc) by using specific organ metabolic rates (ie, organ REE/mass). Results: Weight loss was 9.5 6 3.4 kg (8.0 6 2.9 kg FM and 1.5 6 3.1 kg FFM). Decreases in REE (28%), free triiodothyronine concentrations (28%), muscle (23%), heart (25%), liver (24%), and kidney mass (26%) were observed (all P , 0.05). Relative loss in organ mass was significantly higher (P , 0.01) than was the change in low metabolically active FFM components (muscle, bone, and residual mass). After weight loss, REEm 2 REEc decreased from 0.24 6 0.58 to 0.01 6 0.44 MJ/d (P = 0.01) and correlated with the decrease in free triiodothyronine concentrations (r = 0.33, P , 0.05). Women with high adaptive thermogenesis (defined as REEm 2 REEc , 20.17 MJ/d) had less weight loss and conserved FFM, liver, and kidney mass. Conclusions: After weight loss, almost 50% of the decrease in REEm was explained by losses in FFM and FM. The variability in REEm explained by body composition increased to 60% by also considering the weight of individual organs.Am J Clin Nutr 2009;90:993-1001.