Human amniotic fluid stem cells (hAFSCs) are a very promising new type of fetal stem cells with numerous applications for basic science and cell-based therapies. They harbor a high differentiation potential and a low risk for tumor development, can be grown in large quantities and do not raise the ethical concerns associated with embryonic stem cells. RNA interference (RNAi) is a powerful technology to explain specific gene functions and has important implications for the clinical usage of tissue engineering. We provide a straightforward, 72-h-long protocol for siRNA-mediated gene silencing in hAFSCs. The lipid-based forward transfection protocol described in this article is the first RNAi approach for prolonged gene knockdown in hAFSCs. This protocol allows efficient, functional and reproducible gene knockdown in human stem cells over a prolonged period of time (approximately 2 weeks). We also show the successful use of this protocol in primary nontransformed nonimmortalized fibroblasts, cervical adenocarcinoma cells, transformed embryonic kidney cells, immortalized endometrial stromal cells and acute monocytic leukemia cells, suggesting a wide spectrum of applications in various cell types.