Background: The eNOS 894G/T polymorphism (GG, GT, and TT) is associated with cardiovascular mortality and may influence cardiovascular diseases as a genetic risk factor. Moreover, this polymorphism has an impact on intraoperative hemodynamics during cardiac surgery with cardiopulmonary bypass (CPB). In this study, we analyzed the influence of this gene polymorphism on early clinical outcome in patients who underwent cardiac surgery with CPB. Also, we performed a 5-year follow-up, assessing the impact of this polymorphism on long-term mortality. Method: 500 patients who underwent cardiac surgery with CPB between 2006 and 2007 were included in this prospective single centre study. Genotyping for the eNOS gene polymorphism was performed by polymerase chain reaction amplification. Results: Genotype distribution of 894G/T was: GG 50.2%; GT 42.2%; TT 7.8%. Cardiovascular risk factors were equally distributed between the different genotypes of the eNOS 894G/T polymorphism. No significant difference among the groups was shown regarding Euroscore, SAPS II and APACHE II. Perioperative characteristics were also not affected by the genotypes, except for the consumption of norepinephrine (p = 0.03) and amiodarone (p = 0.01) which was higher in the GT allele carrier. The early postoperative course was quite uniform across the genotypes, except for mean intensive care unit length of stay which was significantly prolonged in GT carriers (p = 0.001). The five-year follow-up was 100% complete and showed no significant differences regarding mortality between the groups.