Literature data concerning the characteristics of metabolic profile in case of various gynecological diseases and pregnancy complications, in particular of endometriosis, polycystic ovary syndrome, infertility, premature birth, preeclampsia, placental insufficiency has been analyzed. Absence of clinically significant biochemical markers of prediction of these diseases has been proved. Search for clinically significant metabolites as markers of the humans’ metabolism will allow identify the disease at the stage of prognosis and increase the treatment effectiveness. Use of metabolomics principles in obstetrics and gynecology is a perspective way for scientific research.