Proteomic analysis of amniotic fluid cells may lead to the discovery of novel markers for embryonic abnormalities. A two-dimensional database for proteins of normal human amniotic fluid cells was constructed. The amniotic fluid cell extract was analyzed by two-dimensional gel electrophoresis and the proteins were identified by matrix-assisted laser desorption ionisation-time of flight-mass spectrometry. The database comprises 432 different gene products, which are in the majority enzymes, structural proteins, heat shock proteins, and proteins related to signal transduction. The obtained data show that the amniotic fluid population maybe either heterogeneous, originating from different fetal compartments and embryo tissues or is still pluripotent. Many proteins which are known to belong to certain cell types were found in the amnion cell fluid. This indicates that some types of fetal cells are already differentiated at the time of amniocentesis (about the 16(th) week of gestation). Moreover, the finding of proteins highly expressed in embryonic stem cells suggests that amniotic fluid could be used as a cell pool for transplantation therapy.