In future, the characterization and isolation of different human stem cells will allow the detailed molecular investigation of cell differentiation processes and the establishment of new therapeutic concepts for a wide variety of diseases. Since the first successful isolation and cultivation of human embryonic stem cells about 10 years ago, their usage for research and therapy has been constrained by complex ethical consideration as well as by the risk of malignant development of undifferentiated embryonic stem cells after transplantation into the patient's body. Adult stem cells are ethically acceptable and harbor a low risk of tumor development. However, their differentiation potential and their proliferative capacity are limited. About 4 years ago, the discovery of amniotic fluid stem cells, expressing Oct-4, a specific marker of pluripotent stem cells, and harboring a high proliferative capacity and multilineage differentiation potential, initiated a new and promising stem cell research field. In between, amniotic fluid stem cells have been demonstrated to harbor the potential to differentiate into cells of all three embryonic germlayers. These stem cells do not form tumors in vivo and do not raise the ethical concerns associated with human embryonic stem cells. Further investigations will reveal whether amniotic fluid stem cells really represent an intermediate cell type with advantages over both, adult stem cells and embryonic stem cells. The approach to generate clonal amniotic fluid stem cell lines as new tools to investigate molecular and cell biological consequences of human natural occurring disease causing mutations is discussed.