Background Endothelial cell nitric oxide synthase (eNOS), vascular endothelial growth factor (VEGF) and hypoxic inducible factor 1- (HIF-1) are important regulators of endothelial function which plays a role in the pathophysiology of heart failure (HF). Prostaglandin E-1 (PGE-1) analog treatment in patients with HF elicits beneficial hemodynamic effects but the precise mechanisms have not been investigated. Methods We have investigated the effects of the PGE-1 analog alprostadil on eNOS, VEGF and HIF-1 expression in human vascular cells (HUVEC) using reverse transcription PCR and immunoblotting under normoxic and hypoxic conditions. In addition, we studied protein expression by immunohistochemical staining in explanted hearts from patients with end-stage heart failure treated or untreated with systemic alprostadil. Results Alprostadil causes an upregulation of eNOS and VEGF protein and mRNA expression in HUVEC and decreases HIF-1. Hypoxia potently increased eNOS, VEGF and HIF-1 synthesis. The alprostadil-induced upregulation of eNOS and VEGF was prevented by inhibition of mitogen activated protein kinases with PD98056 or UO126. Consistently, the expression of eNOS and VEGF was increased and HIF-1 reduced in failing hearts treated with alprostadil. Conclusion The potent effects of alprostadil on endothelial VEGF and eNOS synthesis may be useful for patients with heart failure where endothelial dysfunction is involved in the disease progress.