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: GriceLC (35% of carbohydrate and 60g of raw rice powder per day) and GflaxLC (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 GriceLC and 40 ± 9 years to GflaxLC. Both groups experienced weight loss and systolic blood pressure reduction. A decrease in inflammatory markers (CRP and TNF-α) was observed after flaxseed intake (mean decrease of 25% and 46% for GflaxLC respectively). All groups also showed improvement in levels of total cholesterol, LDL-c, uric acid and adiponectin. Only GflaxLC 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-α. TRIAL REGISTRATION: ClinicalTrials.gov NCT02132728.