Although triglycerides (TG) are a major risk factor for coronary artery disease (CAD), their exact role is still controversial. Recently, a T/C polymorphism in the promoter region of the apoA5 gene at position 1131 has been found that is associated with an increased plasma TG concentration. We investigated the role of this polymorphism in 308 Hungarian patients with CAD referred to coronary bypass surgery, and in 310 controls recruited from the same area. The prevalence of the apoA5-1131C allele was significantly higher among CAD patients than among controls (10.9% versus 5.7%; P < 0.001, Odds ratio (OR) = 1.99 (1.30-3.04)). Controls carrying the rare C allele had in average 23.0% (P < 0.001), subjects with CAD 13.8% (P < 0.001) higher TG levels compared to common allele homozygotes. The polymorphism was not associated with other conventional CAD risk factors or laboratory data of the patients. In logistic regression models adjusted for age, gender, presence of diabetes, BMI, smoking, LDL-C, HDL-C and hypertension a significantly increased risk of developing CAD was found in patients carrying the apoA5-1131C allele (P < 0.001; OR = 1.98 (1.14-3.48)), suggesting that this allele variant is an independent genetic risk factor for CAD.