Endometriosis, the presence of ectopic endometrium, has an unclear etiology and is commonly associated with endocrine, genetic, and immunological imbalance. This study determined whether immunomodulation by the RESAN vaccine could alter the potentially pathogenic gene expression profiles in the cells of the eutopic endometrium in an animal model of endometriosis. Preventing these changes could inhibit the early development of the illness and support the success of surgical treatment. Wistar rats were divided into three groups: prophylaxis (vaccinated before ectopic endometrium implantation, n = 23), therapeutic (vaccinated at the time of the ectopic excision, n = 23) and control (n = 10). During the first laparotomy, autotransplantation of the endometrium to the peritoneum was performed in the prophylaxis and therapeutic groups. The second laparotomy was carried out three months later in all groups to examine endometriotic foci and adhesions. Suspected endometriosis foci were removed. Three months later, the third laparotomy was performed in all animals, followed by suspected foci excision. Fragments of the eutopic endometrium were collected from all animals during the first and third laparotomies. All samples were analysed by real-time PCR to assess the expression of Bcl2, Bax, Bax/Bcl2 ratio, Mki67, and Tert genes. Endometrial foci were found in abdominal peritoneum at the second laparotomy in 1 animal in the prophylaxis group, compared to 16 animals in the therapeutic group. The prophylaxis group showed a high expression of Bax while the therapeutic group showed high expression of Bax, Tert and Mki67 genes. Additional analysis revealed that throughout the six months of the experiment, the expression of the Bax, Tert, and Mki67 genes decreased significantly in the prophylaxis group, Mki67 gene expression decreased in the therapeutic group, and Tert, Mki67, and Bcl2 gene expression decreased in the control group. The results indicate that immunomodulation affects the balance between apoptosis and proliferation in the eutopic endometrium and may prevent the onset and recurrence of endometriosis.