Objective To find out the best injection method of the bone marrow mesenchymal stem cells (BM-MSCs) transplantation in the treatment of a rat model with hind limb arterial ischemia. Methods Twenty-four SD rats were randomly divided into four groups: normal control group, model group, BM-MSCs acupoint injection group (Al group) and BM-MSCs muscular injection group (Ml group). Acupoints of "Sanyinjiao"(三阴交 SP 6) , " Housanli" (后三里 ST 36), "Zhaohai" (照海 Kl 6), "Huantiao" (环跳 GB 30) and "Yanglingquan" (阳陵泉 GB 34) were selected for Al group, and five nonacupoints were selected on gastrocnemius and adductor of ischemic hind limbs in the Ml group. BMMSCs were injected to the latter two groups. The ischemic hind limb rat model was established using the method of blocking the femoral artery and its branches. The changes of blood flow (perfuse unit, PU) in the affected hind limb and the healthy hind limb were consecutively monitored with laser Doppler flowmetery. The PU index (PUI, the PU ratio of the affected hind limb to the healthy hind limb blood perfusion to describe the visual increment of the blood flow. Besides, the levels of vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) were detected, and the expressions of VEGF and bFGF were observed by immunohistochemical semiquantitative analysis. Results Compared with the model group and the Ml group, the PUI was significantly higher in the Al group on the 3^rd, 14^th and 21^st day after injection of BM-MSCs (P〈0.05, P〈0.01). Compared with the model group, the serum VEGF, bFGF levels and the immunohistochemical expressions of VEGF and bFGF in the Al and Ml groups were significantly increased (all P〈0.01). Conclusion After injection of BM-MSCs through the acupoint, the recovery speed of perfusion in the ischemic rat hind limbs was fast. Compared with the muscular injection, it can significantly improve the blood flow in the ischemic r