It is known that bone formation and bone remodelling would not occur unless there is already a proper established micro/vasculature. However, blood vessels can be damaged by extrinsic causes like chemotherapeutic agents. Methotrexate (MTX) is an anti-metabolite chemo-agent which is widely used in treatment of many diseases including childhood leukaemia and inflammatory disorders. While previous studies showed that MTX can cause long-term skeletal side effects, whether and how it damages bone marrow (BM) micro vasculature remains unclear. In addition, since we have recently shown that osteogenic and anti-inflammatory flavonoid genistein can protect bone in MTX-treated rats, it is unknown if it prevents MTX-induced blood vessel damages or enhances recovery. Cell culture MTT assays showed that viability of rat primary sinusoid endothelial cells (SECs) was reduced by MTX in a concentration-dependant manner (10nM-10μM) following 48h MTX treatment. Flow cytometry analysis revealed that SECs underwent apoptosis following 48h treatment with MTX (1μM). MTT assays also showed that genistein (1μM and 100nM) did not affect viability of SECs. Tube formation assays showed a reduced tube formation potential of SECs treated with MTX (1μM), genistein-treated SECs showed enhanced tube formation, and genistein treatment can prevent MTX-induced decrease in tube formation. In rats treated with 5 daily MTX (0.75mg/kg), histological image analyses of tibial sections showed significant BM blood vessel damages on day 6 and day 9 (after the 1st MTX dose) and significant but partial recovery on days 11 and 14. However, genistein co-treatment attenuated MTX-induced blood vessel damages and it enhanced VEGF expression in the bones. Consistently, genistein-treated SECs also produced more VEGF and more tubes were formed when SECs were treated with conditioned medium of SECs pre-treated for 24h with genistein. Therefore, genistein seems to a potent natural compound to be able to protect and/or enhance recovery of micro-blood vessels following MTX-therapy.