This study describes the first promising steps in the comparison of peptide patterns of laser capture microdissected trophoblast cells obtained from frozen tissue sections in relative low numbers, approximately 125 cells. Trophoblasts were collected by laser capture microdissection from a terme human placenta and dissolved in detergents, sonified, and digested with trypsin. The resulting peptide mixtures were directly analyzed by matrix-assisted laser desorption/ionisation-time of flight mass spectrometry. Using this approach specific peptide patterns that consist on average of approximately 35 peptide peaks for trophoblast cells, and surrounding villous stroma cells could be obtained. From the results it was concluded that trophoblast and surrounding villous stroma cells show exclusive discriminating peptide patterns. In the future this method is potentially suitable for finding specific peptides and identification of proteins that are related to the pathogenesis of trophoblast pregnancy diseases such as preeclampsia.