Abortion is categorized as the termination of conception caused by the failure or removal of the embryo from the uterus before the conclusion of pregnancy. Microorganisms and genetic factors are two of the many factors associated with abortion. Cytomegalovirus is a widespread congenital virus infection pathogen that affects a wide variety of people. The prothrombin gene is one of the essential causes that trigger blood clotting and the function of abortion women, therefore the aim of the study is to detect and associate Cytomegalovirus and prothrombin gene mutation (Gene ID: 14061 in NCBI) with abortion through genetic and immunological methods. Five ml of whole blood was collected from an intravenous puncture and divided into two tubes, one with EDTA and one without (plain tube) from 74 women with an abortion history as a patient group and 74 women without an abortion record who had at least one successful fertility as a control group. Allele-specific PCRs are used to amplify gene regions with genetic primers containing prothrombin gene polymorphisms. Current results have shown the greatest risk of abortion was observed in women patients with IgG seropositivity in 65 women with frequency (87.8%) and the lowest rate of abortion was in IgM seropositivity in 3 women with frequency (4.1%) and 6 (8.1%) were positive for IgM-and IgG indicating they have both an old and recent infections. Furthermore, allele-specific PCRs are used to amplify prothrombin G20201A polymorphism. The result of this study demonstrated there is no association between prothrombin genotype level frequency and abortion in CMV-infected women. While, there is a highly significant association between A and G Alleles combinations and abortion in CMV-infected women.