Missed abortion is one of the most prevalent forms of early pregnancy loss that remains a pressing issue of obstetrics and gynecology. Despite advances in reproductive medicine, the molecular mechanisms underlying the embryo development termination in early gestation are poorly understood. A comparative singlecenter study aimed to assess the expression of TGF-β and MMP-9 genes in peripheral blood of women with physiological and missed abortion and assess their potential prognostic value for evaluation of the risk of early pregnancy loss. A total of 40 pregnant women were included in the study: 20 patients with the 9–11 week physiological pregnancy (control group) and 20 women diagnosed with missed abortion (index group). The TGF-β and MMP-9 gene expression was determined by the real-time polymerase chain reaction method after the total RNA isolation from peripheral blood. The Mann‒Whitney U-test and ROC analysis were used for statistical data processing. No significant differences in the TGF-β and MMP-9 gene expression between the studied groups were revealed. At the same time, ROC analysis made it possible to determine the threshold values of the studied indicators having some diagnostic information content. As for MMP-9, the threshold value Ct ≤ 29 ensuring the 80% sensitivity and 60% specificity turned out to be the most informative. As for TGF-β, the threshold value Ct ≤ 27.4 was characterized by the 75% sensitivity and 70% specificity. The findings suggest the potential prognostic value of the studied genes for evaluation of the risk of missed abortion.