Background: For patients with thromboangiitis obliterans (TAO), revascularization with bypass or angioplasty is frequently not feasible due to the poor outflow of the distal small vessels. We evaluated the long-term results of our experience treating patients with TAO with autologous bone marrow-derived mononuclear cells (ABMMNCs) to determine the safety and efficacy of ABMMNC therapy in patients with critical limb ischemia due to TAO. Methods: This was a retrospective chart review from a single university hospital vascular surgery center between January 2005 and July 2006. Patients were treated with smoking cessation and either aspirin (100 mg/day) alone or aspirin and ABMMNC injection according to patient preference. Groups were compared for demographics, clinical characteristics, and short-term and long-term results. Results: Of 59 patients with TAO who were treated, 19 patients elected aspirin alone and 40 patients elected aspirin and ABMMNC injection. No patients suffered perioperative complications and 49 (83%) patients remained smoke-free for 10 years. The 10-year amputation-free survival was 85.3% (29/34) in patients treated with ABMMNCs compared to 40% (6/15) in patients treated with aspirin alone (p = 0.0019). Ulcer area (p < 0.0001), toe-brachial index (TBI; p < 0.0001), transcutaneous oxygen pressure (TcPO2; p < 0.0001), and pain score (p < 0.0001) were also significantly improved with ABMMNC treatment, although there was no difference in mean ankle-brachial index (ABI; p = 0.806). Conclusions: In patients with critical limb ischemia due to TAO, ABMMNC treatment was safe and effective. ABMMNC treatment significantly improved amputation-free survival, ulcer healing, and pain, although there is no difference in ABI compared to treatment with aspirin alone.