ObjectiveTo compare the anti-apoptotic potency of human mesenchymal stem cells (hMSCs) derived from patients with cyanotic congenital heart diseases (C-CHD) or acyanotic congenital heart diseases (A-CHD) in vitro and explore the possible mechanism. MethodshMSCs were isolated from patients with cyanotic (Group C) or acyanotic (Group A) congenital heart diseases and cultured in a hypoxic incubator (1% O2, 5% CO2, 94% N2) in vitro. The anti-apoptotic potency of the hMSCs was assayed by the Annexin V-FITC/PI double labeled flow cytometry. The content of B-cell lymphoma-2 (Bcl-2), Bax and caspase-3 in both groups was determined by Western blot. ResultsFlow cytometry results revealed that hMSCs from C-CHD patients presented higher level of resistance to ischemia-and anoxia-induced apoptosis with lower overall (P<0.05) and early apoptosis ratio (P<0.01). Further Western blot examination identified that C-CHD-derived hMSCs produced more Bcl-2 (P<0.05) but less Bax (P<0.05) and caspase-3 (P<0.05) in comparison to their A-CHD-derived ones. ConclusionC-CHD-derived hMSCs presented the superiority for the anti-apoptotic potential, and the possible mechanism is the favorable change of Bcl-2, Bax and caspase-3 induced by the natural hypoxic and anoxic precondition.