Endothelial regeneration and dyslipidemia impair endothelium-dependent relaxation, while supplementation with fish oil (FO) prevents it. The genomic impact of different diets was compared in primary cultures derived from native and regenerated endothelial cells. Pigs were fed with high-cholesterol (CHL) or FO-rich diet. Partial in vivo removal of endothelium was performed to induce endothelial regeneration. Native and regenerated cells were harvested, cultured, and prepared for genomic (microarray experiments, real-time PCR) and proteomic (Western blotting) analysis. The analysis identified genomic changes induced by chronic CHL diet in native cultures resembling those induced by in vivo regeneration, as well as those that could be prevented by FO diet. At the protein level, the reduced and increased presences of endothelial nitric oxide synthase and F2, respectively, observed after regeneration combined with CHL diet were alleviated by FO. The comparison of the differential changes induced by regeneration in vivo in endothelial cells from both diet groups revealed a limited number of genes as the most likely contributors to reduction in endothelium-dependent relaxations in porcine coronary arteries lined with regenerated endothelium.