•The first study comparing cytokine concentration, expression of CD47 and CD274 immunosuppressive proteins on HSCs in bone marrow and blood of hematopoietic stem cells donors.•Concentration of proinflammatory cytokines is higher in blood than in bone marrow.•TGFβ is present at very high concentrations in bone marrow.•High level of IL-10 was detected in peripheral blood of G-CSF stimulated donors.•CD47 protein expressions is higher in bone marrow than in peripheral blood. Cytokine composition of bone marrow microenvironment in comparison to blood is poorly explored. The goal of this study was to investigate the levels of cytokines present in peripheral blood and bone marrow of healthy hematopoietic stem cells donors. The data obtained on this subject with addition to cytometric analysis can provide new insight into the hematopoietic stem cells microenvironment. Study consisted of cytokine concentration analysis performed by ELISA tests of peripheral blood of healthy peripheral blood stem cells donors and bone marrow of healthy bone marrow donors. Additionally we have tested the expression of CD47 and CD274 proteins on the surface of hematopoietic stem cells by the flow cytometry analysis. The results has shown different composition of analyzed cytokines (IL-1 β, IL-2, IL-4, IL-6, IL-10, IL-17A, TGF-β1, IFN-γ and TNF-α) present in bone marrow and blood of stem cells donors. The hematopoietic stem cells in peripheral blood are subjected to higher levels of proinflammatory cytokines whilst the lower level of those cytokines in bone marrow with a very high level of TGF-β1 which possibly creates a more immunosuppressive environment. The IL-10 level was significantly higher in peripheral blood of PBSC donors after the administration of mobilizing factor (G-CSF). The percentage of CD47+HSCs was significantly higher in bone marrow compared to peripheral blood of mobilized donors.