Most of the researchers attribute amniotic fluid stem cells (AF SCs) to mesenchymal stem cells (MSCs). However, AF SCs express both mesenchymal and epithelial markers, which distinguishes them from postnatal MSCs. Cultivation in the three-dimensional matrix provides a different look at the nature of these cells. We showed that, in 3D collagen gel, AF SCs form epithelial structures (tubules and cysts). Active contraction of the gel during the first days of cultivation, which is characteristic if mesenchymal cells, does not occur. Electron microscopic study showed that typical to epithelial cell adherent junctions are formed between AF SCs. On the other hand, AF SCs continue to express MSCs markers during cultivation in the gel. Thus, AF SCs may not be true mesenchymal cells because they can display properties of epithelial cells. Perhaps these cells undergo epithelial-mesenchymal transition, the process which actively takes place during embryogenesis.