In the сlinical practice, allogeneiс bone marrow transplantation (BMT) is often cause of the graft-versus-host disease (GvHD). GvHD is explained by the fact that T-lymphocytes, which are administered simultaneously with hematopoietic cells during transplantation and after then formed and matured in the timus of the recipient from donor progenitor cells, recognize and attack the cells of the host. However, a complete explanation of the phenomenon of the GvHD does not exists, and the chimerization of the recipient’s organism as a possible cause of damage of its organs is not taken into account. Therefore, the aim of this work was the modeling of allogeneic transplantation of the whole bone marrow (BM, experiment) and comparing its results with syngeneic transplantation (control) basing on the investigation of engraftment of cells of donor origin in the main GvHD target organs. Bone marrow (BM) donors were Tg(ACTB-EGFP)1Osb/J mice carrying a green fluorescent protein gene (EGFP), recipients were the animal of CBA and C57BL/6 inbred strains with age 2–10 months. 1 day before BMT (1.5×107 cells per mouse) all recipients were irradiated at a dose of 6.5 Gy (LD 50/30). After 1, 3, 5, 7, 11, 14, 21, 28, 35 and 55 days the development of chimerism in the liver, skin and colon of animals was examined using a fluorescent microscope. Already in 1 day, single fibroblast-like donor cells were found in the colon, in 7 days – in the skin and liver. 14–28 days after BMT, with donor cells mainly stroma in the liver, in the skin fibroblasts and keratinocytes were formed, in the colon villous cells and also stromal and parenchymal cells of Peyer’s patches which were died off after irradiation were substituted. Unlike control, in the experimental groups GFP+ giant fibroblasts about 30 mkm in length were found in the stroma of the liver, in the skin and in the colon; in the liver there was a lot of GFP+-bulkheads and fibroblast-like Ito’s cells of a very intricate configuration. To 35–55 days after allogeneic BMT cells of the donor origin in the liver and in the villi of the colon began to destroy, the villi became overgrown with GFP+-connective tissue cells and warped, wall of the colon became thin and the skin was fully substituted with a new one (all these things were never observed in the conrol groups). We propose a hypothesis that beside with GvHD traits like thinning of the colon wall and plenty of roundish GFP+-cells on inner surface of the skin, other signs of the studied after allogeneic BMT organs suggest that the cells of the organs which are formed from mesenchymal stem cells of the whole bone marrow become target for the recipient’s T-cells, i.e. suggest existence of host-versus-graft (HVG) reaction. Obvious manifestation of immune reactions after BMT directly coincides with the term of massive engraftment of the studied organs with cells of donor origin and restoration of the host’s own immune system, i.e. the development of chimerism determines the development of organ damage. This explains the events of GvHD from medical practice – atrophy of the mucous membranes, excess production of collagen, sclerosis of the bile ducts, skin damage, colitis – and the timing of its manifestation.