Objective To investigate the effect and safety of autologous bone marrow-mononuclear cell (BM-MNC) transplantation on ischemic limb of patients with thromboangiitis obliterans (TAO). Methods Thirteen patients with TAO underwent transplantation of autologous BM-MNC into ischemic muscles of 17 lower limbs. A series of subjective indexes (improvement of pain and cold sensation) and objective indexes including increase of ankle brachial index (ABI), transcutaneous oxygen pressure (TcPO2), and improvement of foot skin ulcer were used to evaluate the effects. Results The outcomes were evaluated after 2 months of transplantation. The pain relief and improvement of cold feeling were in 15 limbs and 16 limbs, respectively. Before transplantation and 2 months after transplantation, ABI was 0.37±0.06 and 0.50±0.17, respectively (Plt;0.05), and TcPO2 of the ischemic legs were (24.59±3.36) mm Hg (1 mm Hg=0.133 kPa) and (35.00±10.44) mm Hg, respectively (Plt;0.05). ABI increased in 9 limbs. TcPO2 elevated in 14 limbs. Skin ulcer improved in 7 limbs. Thirteen patients were followed up from 4 to 18 months (average 8 months), the patients’ symptoms improved in 13 limbs. ABI was 0.45±0.14, which wasn’t different from those before transplantation and 2 months after transplantation (Pgt;0.05). TcPO2 was (33.24±10.43) mm Hg, which was different from those before transplantation and 2 months after transplantation (Plt;0.05) and was elevated in 12 limbs. Skin ulcer healing was in 5 limbs. The ischemic symptoms in 2 patients were not relieved. There was no mortality and high level amputation. The following complications, such as proliferative retinopathy, malignant tumor, myocardial infarction, stroke or hemangioma, were not found in all patients.Conclusion In patients with TAO, intramuscular transplantation of autologous BMMNC is a safe and effective method, and may improve symptoms and accelerate the healing of skin ulcer.