In the study we aimed to estimate the number of functional MSCs by performing colony-forming unit-fibroblast (CFU-F) cultures from pediatric hematopoietic stem cell transplantation recipients and their healthy donors. Secondly we compared the concentration of cytokines interleukin 2 (IL-2), IL-4, IL-10 and tumor necrosis factor α (TNF-α) in stem cell serum and in supernatant of mesenchymal stem cell cultures. We included into the study 19 consecutive pairs of donors and recipients of allogeneic stem cell transplantation from one pediatric bone marrow transplantation center. Cultures of mesenchymal stem cells were performed according to the research protocol for enumeration of human mesenchymal progenitor cells using the CFU-F assay and the expansion of human mesenchymal cells in vitro (StemCell Technologies, USA). Interleukin 10 and TNF-α concentration were measured by high sensitivity (Quanikine HS) human immunoassay (R&D and Bender, USA). Interleukin 2 and IL-4 concentration were assessed by human IL-2 ELISA Version 2 assay (Bender MedSystems, Austria). The number of CFU-F colonies in cultures increased with the dose of mononuclear cells given, but the difference between donors and recipients was not significant. The TNF-α level significantly decreased, and IL-10 and IL-2 increased in CFU-F supernatant as compared to stem cell serum. The concentration of IL-4 was higher in CFU-F cultures, although p value in donors was not significant. We concluded from the study that the immunomodulatory effect of donor and recipient MSCs may partially depend on secretion of IL-2 and IL-10 and inhibition of TNF-α secretion.