This study sought to determine whether exercise training or weight loss could affect altered fatty acid oxidation (FAO) in the skeletal muscle of obese individuals using both cross-sectional and longitudinal designs. The cross-sectional design compared extremely obese women after weight loss via gastric bypass surgery [body mass index (BMI): 36.5 ± 3.5 kg/m2] to extremely obese individuals [BMI: 50.7 ± 3.9 kg/m2] as well as to lean individuals [22.8 ± 1.2 kg/m2]. The longitudinal design examined the effect of exercise training on muscle FAO in these three groups. The authors found that exercise training enhanced the ability to oxidize lipids in the skeletal muscle of individuals where lipid oxidation was initially depressed (previously extremely obese subjects) to the same extent as in lean individuals. In contrast, substantial weight loss (approximately 50 kg) did not normalize the deficit in lipid oxidation observed in the skeletal muscle of extremely obese individuals. These findings suggest that clinical weight loss and exercise training interventions have distinct effects on the lipid oxidation potential in the skeletal muscle of obese individuals.