Objective To compare the effectiveness of autologous implantation between bone marrow stem cells and peripheral blood stem cells for treatment of lower limb ischemia. Methods From December 2004 to December 2005, 42 patients with unilateral lower limb ischemia were treated with both autologous bone marrow stem cell implantation(group A, n=21)and autologous peripheral blood stem cell implantation (group B, n=21). Fortytwo patients included 32 males and 10 females. The age ranged from 34 to 80 years, with a mean of 65.6 years. Of the patients, there were 28, 8 and 6 patients suffered from diabetic lower limb ischemia, Burger’s disese and atherosclotic occlusion, respectively. Ischemic history was from 3 months to 5 years, with amean of 2.1 years. A series of subjective indexes (such as improvement of pain, cold sensation and numbness) and objective indexes such as increase of ankle brachial index (ABI), transcutaneous oxygen pressure (TcPO2), angiography, amputation rate, and improvement of foot wound healing, were used to evaluate the effect. Results After 4 weeks of implantation, the rate of pain relief was 88.2% in group A and 89.5% in group B (Pgt;0.05) ; the rate of cold sensation relief was 94.4% in group A and 94.7% in group B（Pgt;0.05）; improvement of numbness was 69.2% and 66.7% respectively in groups A and B（Pgt;0.05）. Increaseof ABI was 38.1% in group A and 33.3% in group B（Pgt;0.05）; increase of TcPO2 was 85.7% and 90.5% respectively in groups A and B（Pgt;0.05）; angiography was performed in 12 patients (group A) and 9patients (group B), and the new formed collateral vessel rate was 83.3% in group A and 77.8% in group B（Pgt;0.05）; the amputation rate was 9.1% in groups A and B（Pgt;0.05）; the rate of improvement of foot wound healing was 60.0% in group A and 66.7% in group B(P＞0.05). Forty patients were followed up 3-15 months(mean 8 months). The improvement rate of subjective symptoms was 75.0% in group A and 70.0% in group B (Pgt;0.05); increase of ABI was 60.0% in group A and 65.0% in group B; increase of TcPO2 was 80.0% and 75.0% respectively in groups A and B; the new formed collateral vessel rate was 90.0% in group A and 84.6% in group B. All ulcers healed except 1 case in group B. Conclusion Bone marrow stem cell graft and peripheral blood stem cell graft are all effective in treatingower limb ischemia.