n-3 and Trans fatty acids are considered to be the important modifiable factors of the metabolic syndrome. The purpose of this study was to test the hypothesis that lower Omega-3 fatty acids and/or higher trans fatty acids of erythrocytes (RBC) are associated with the risk of the metabolic syndrome. Forty-four patients with the metabolic syndrome, defined by three or more risk factors of the modified Adult Treatment Panel III criteria, and eighty-eight age- and sex-matched controls with less than three risk factors were recruited for the study. The mean age was 54.5 (sem 0.8) years and 45 % of subjects were female. Trans fatty acids of RBC were higher in patients than controls (0.82 (sem 0.04) v. 0.73 (sem 0.03) %; P = 0.043), while their Omega-3 indexes, the sum of EPA and DHA in RBC, did not significantly differ (11.78 (sem 0.04) v. 12.39 (sem 0.02) %). Multivariable-adjusted regression analysis showed positive association between trans fatty acid and risk of the metabolic syndrome (OR 7.13; 95 % CI 1.53, 33.27; P = 0.013). Fasting serum insulin (7.9 (sem 0.7) v. 4.9 (sem 0.3) muU/ml; P < 0.001) and high sensitivity C-reactive protein (18 (sem 3) v. 11 (sem 17) mg/l; P = 0.042) were also higher in patients than controls. There were significant positive relationships between trans fatty acids and waist circumference, and between trans fatty acids and BMI. The results suggested that RBC trans fatty acids might be a predictor of increased risk for the metabolic syndrome, but n-3 fatty acids were not in this population.