Background: Obesity is a public health problem affecting 35% of the adult population in the US.A 5-10% weight loss decreases the risk of cardiovascular disease and diabetes mellitus. Diet and exercise have shown to be effective in the treatment of obesity, but adherence is a limitation. Dark chocolate (DC) polyphenols were proven to have beneficial effects on blood pressure, endothelial function, HDL cholesterol, lipoprotein ratios and inflammation markers. Also, it might play a role in improving fat metabolism and satiety; however, its effects on weight loss are still not clear. We propose a protocol to explore the effects of DC associated with hypocaloric diet and exercise on weight loss during a 12-week period in obese adults. Methods and Design: The study is a randomized controlled trial with 2 parallel arms comparing hypocaloric diet + exercise with hypocaloric diet + exercise + 50g dark chocolate/day during a 12 week period. A total of 408 obese adults (18 to 45 years old) with no comorbidities that could compromise the exercise program will be recruited. Primary outcome is proportion of patients who had 5% or more weight loss after 12 weeks. Secondary outcomes are glucose levels and insulin resistance (HOMA-IR), lipid profile, abdominal circumference, body fat mass (estimated by skinfold thickness) and blood pressure, satiety perception and drop-out rates. Primary outcome (percentage of patients achieving 5% or more weight loss) will be analyzed by chi-square test with an Intention-to-Treat approach. Conclusions: This phase II randomized controlled trial has the aim to explore the effects of including dark chocolate as an adjuvant to classical therapies (hypocaloric diet and exercise) on weight loss in a 12-week period Trial registration: the trial will be registered at www.clinicaltrials.gov