Induction of apoptosis represents a potential reaction of endothelial cells (ECs) after injury of the vascular endothelium. Beneficial effects of n-3 polyunsaturated fatty acids (PUFAs) in vascular diseases are widely recognized although the responsible mechanisms are not fully understood. Because it is not known whether PUFAs modulate EC apoptosis, we investigated the effects of n-3 and n-6 PUFAs on 4-hydroxynonenal (HNE)-induced EC apoptosis by Annexin V-staining and caspase-3 activation assays. Pre-treatment with the n-3 fatty acid docosahexaenoic acid (DHA) reduced HNE-induced EC apoptosis. DHA-treated cells did not show the pronounced drop in intracellular GSH after HNE-exposure seen in vehicle- or n-6 arachidonic acid (AA)-treated cells. This is most likely due to increased GSH levels in DHA-treated cells. Furthermore, DHA pre-treatment increased ciap1 mRNA levels and transfection of ciap1 siRNA abolished the protective effect of DHA in HNE-induced apoptosis in HUVECs. Thus, pre-treatment of HUVECs with DHA reduces HNE-induced oxidative stress and apoptosis and the protective effects of DHA seem to be dependent on cIAP1. The results provide a possible new mechanism for the atheroprotective effects of n-3 fatty acids in vascular disease.