To determine the possible role of the common FABP1 T94A polymorphism in modulating susceptibility to traits of the metabolic syndrome, we analysed a random sample of 826 subjects from the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam cohort. Multivariate adjusted linear trend regression analysis of metabolic, anthropometric and blood pressure variables in FABP1 T94A genotypes were performed in both genders. In women, a significant trend of higher plasma triglyceride (P=0.01) and LDL-cholesterol (P=0.02) concentrations were seen for A-allele carriers after adjustment for age, menopausal status, hormone intake and Apo E genotype. Because elevated triglyceride and cholesterol levels are important risk factors of cardiovascular disease (CVD) and type 2 diabetes mellitus (T2DM), we additionally analysed the association of the T94A variant and disease risks in two studies enrolling 220 incident CVD and 192 incident T2DM patients of the EPIC-Potsdam cohort. After adjusting for age, sex, BMI and other covariates, we found no association between FABP1 T94A and CVD or T2DM. In conclusion, our study provides evidence for an association of the FABP1 T94A polymorphism and fasting triglycerides and LDL-cholesterol levels in females. These results support previous findings in fenofibrate-treated individuals and thereby provide some additional indication of the functional relevance of the FABP1 T94A SNP in hepatic fatty acid and lipid metabolism in humans.