Analysis of fetal cells and cell-free fetal DNA in maternal peripheral blood raises hopes for development of new non-invasive prenatal diagnosis. Many different cell types were considered as possible targets for prenatal diagnosis. Probably, fetal cells and cell-free fetal DNA enter the maternal circulation during all pregnancies. They may persist for years in maternal blood and tissues, resulting in a physiological microchimerism. It has been shown that changes in these two parameters may accompany some pregnancy-related disorders. Microchimerism is associated with pathology of several autoimmune diseases and diseases which preferentially affect women. However, its long-term consequences are still under investigation. Widespread clinical implications of fetal cells and cell-free fetal DNA as diagnostic tools awaits further research aiming at improvement of insufficiently sensitive techniques.