Down Syndrome is the most frequent genetic cause of mental retardation. Deregulation of specific differentiation processes is a major cause for the neuropathological cell features typical for this syndrome. The molecular mechanisms leading to Down Syndrome are likely to be operative from the very earliest time of embryonic/fetal development. We therefore analysed human amniotic fluid cell samples and cytotrophoblastic cells from placental biopsies, both with normal karyotypes and with trisomy 21, for the mRNA expression of stem cell marker genes. Here we describe for the first time that these human primary cell sources contain cells that express telomerase reverse transcriptase, leukemia inhibitory factor receptor, and bone morphogenetic protein receptor II. A specific difference between aneuploid and normal cells could not be detected. These data provide evidence that human amniotic fluid and cytotrophoblastic cell cultures might provide a new source for research on primary cell systems expressing these stem cell markers. In addition, it is suggested that early deregulation of the expression of these genes in the here analysed cell sources does not contribute to the molecular development of Down Syndrome.