Background: Flaxseed has received attention for its anti-inflammatory and antioxidant role. The present study hypothesizes if flaxseed added to a weight loss diet could improve the lipid and metabolic profiles and decrease risk factors related to cardiovascular disease. Methods: In a prospective, single blinded 42 days protocol, subjects were allocated into two groups with low carbohydrates intake: G(riceLC) (35% of carbohydrate and 60g of raw rice powder per day) and G(flaxLC) (32% of carbohydrate and 60g of flaxseed powder per day). Blood pressure, anthropometric measures and serum levels of isoprostane, C-reactive protein, Tumor Necrosis Factor-alpha, glucose, lipidic profile, uric acid, adiponectin, leptin and insulin were measured at baseline and at the end of interventions. Serum and urinary enterodiol and enterolactione were also measured. Results: A total of 27 men with cardiovascular risk factors were evaluated, with mean age of 33 +/- 10 years to G(riceLC) and 40 +/- 9 years to G(flaxLC). Both groups experienced weight loss and systolic blood pressure reduction. A decrease in inflammatory markers (CRP and TNF-alpha) was observed after flaxseed intake (mean decrease of 25% and 46% for G(flaxLC) respectively). All groups also showed improvement in levels of total cholesterol, LDL-c, uric acid and adiponectin. Only G(flaxLC) group showed a decrease in triglyceride levels. Conclusion: This study suggests that flaxseed added to a weight loss diet could be an important nutritional strategy to reduce inflammation markers such as CRP and TNF-alpha.