OBJECTIVE: To study the biological characteristics of bone marrow-derived mesenchymal stem cells（MSC）in children with aplastic anemia (AA) and evaluate the relationship of biological characteristics of MSC with the efficacy of immunosuppressive therapy (IST). METHODS: Bone marrow- derived MSC were cultured and isolated from 29 children with AA and 5 normal controls. Seventeen out of the 29 cases received IST. Surface markers and cell cycle of MSC at passage 3 were analyzed by flow cytometry. The inhibition of lymphocyte proliferation by MSC was evaluated and TGF-β1 level in the supernatant of MSC was detected using ELISA.ResultsGrowth abnormality of MSC was found in 16 children with AA (55%), characterized by deficiency and poor proliferation of MSC, and was frenquently seen in patients with severe AA or in patients with more prolonged disease course or in patients with radiation/chemotherapy-induced AA. Surface markers, cell cycle and TGF-β1 level in the supernatant of MSC at passage 3 and the inhibition of lymphocyte proliferation by MSC in the AA group were similar to those in the control group. Eight out of nine patients with normal MSC growth achieved complete remission (CR) but only 2 out of 8 patients with abnormal MSC growth achieved CR following IST (P<0.01). CONCLUSIONS: Bone marrow-derived MSC growth abnormality occurs in most of children with AA. MSC abnormality may affect adversely hematological recovery following IST.