The aim of the given project was to assess the influence of previously known factors, as well as the impact of allogeneic stem cell transplantation (SCT), on the presence and characteristics of mesenchymal stromal cells (MSC) in the bone marrow (BM). Previous research demonstrated that a number of factors, such as age, gender, previous illnesses and therapies, affected the presence of MSC. This work confirms these results and in particular the effect of an allogeneic SCT. The examination of factors associated with transplantation revealed a significantly lower MSC count in patients following total body irradiation, as well as a significantly higher cell count in patients with poor engraftment. Growth kinetics revealed a limited proliferative capacity of the MSC after allogeneic SCT. In the observation group MSC were less frequently isolated following SCT compared to baseline. During the observation period no regeneration of the presence of MSC was observed. For the first time it has been demonstrated that allogeneic SCT have a sustained impact on the presence of MSC in the BM.