Introduction Low-carbohydrate, high-protein diets are a current challenge in the nutritional treatment of obesity. Objective To compare the effect of a low-carbohydrate high-protein diet with a traditional hypocaloric diet on weight loss and mitochondrial oxidative metabolism. Subjects and methods Nineteen obese men (age 36 +/- 6 years; body mass index 34 +/- 2 kg/m(2)) were randomized to follow one of the two diets-control diet (15% protein; 30% lipids; 55% carbohydrates) or high-protein diet (30% protein; 30% lipids; 40% carbohydrates)-over an 8-week period. Anthropometry, biochemical variables, resting energy expenditure and mitochondrial oxidation were measured at the start and at the end of the intervention. Results The high-protein diet produced a greater weight loss (- 8.3 +/- 1.2% versus - 5.5 +/- 2.5%, P = 0.012) than the control diet. Interestingly, an activation in the mitochondrial oxidation was found in the high-protein-fed group. This stimulation was positively correlated with the final resting energy expenditure and negatively associated with the final fat mass content. Conclusion Low-carbohydrate high-protein diets could involve specific changes in mitochondrial oxidation that could be related to a higher weight loss.