RNA interference is applied to study gene function in different organisms and in various cell types. Little is known about the effect of RNA interference on human endothelial progenitor cells (EPCs) in vitro. To address this issue, short hairpin RNA targeting the human hypoxia inducible factor-1alpha (HIF-1alpha) was transferred into human EPCs by an adenoviral vector. HIF-1alpha mRNA and protein expression was dramatically and specifically downregulated after adeno-small interfering RNA (siRNA)-HIF-1alpha infection in cells under hypoxia, a condition in which HIF-1alpha would have been induced. This effect persisted for at least 72 h and was accompanied by suppression of vascular endothelial growth factor (VEGF) mRNA and protein expression. The expression of endothelial cell markers CD31, VEGF receptor 2 (Flk-1) and eNOS as well as NO production were also markedly decreased. Functional studies showed HIF-1alpha knockdown via adenoviral siRNA transfer inhibited EPC colony formation, differentiation, proliferation and migration. These data indicate that specific gene knockdown via adenoviral transfer of siRNA is feasible in EPCs, and the effect is long-lasting. Our findings raise the possibility that such long-term modified human EPCs may be used to treat hypoxic tumor metastases that are known to be resistant to conventional therapeutic regimes.