Systemic sclerosis (SSc or scleroderma) is an autoimmune connective tissue disease characterized by diffuse fibrosis, degenerative changes, and microvascular abnormalities. The vasculopathy mainly affects small arteries and capillaries and causes insufficient blood flow, which leads to clinical manifestations, such as Raynaud’s syndrome, fingertip ulcers, and gangrene. Recently, implantation of bone marrow-derived mononuclear cells (MNCs) has been successfully used for therapeutic neovascularization in Buerger’s disease that is thought to be an “autoimmune” vasculitis. The purpose of this study is to determine the efficacy of autologous MNC implantation into the ischemic digits of patients with connective tissue diseases. This study was performed as a prospective, non-randamized, and multicenter clinical trial. Thirty-four patients (19 SSc, 5 SLE, 2 CREST, 2 MCTD, 4 APS, 2 PN) who had painful ischemic digits with skin ulcers were enrolled in this study. Autologous MNCs obtained from bone marrow or peripheral blood were implanted into the ischemic digits. Ischemic pain and ulcers improved remarkably after MNC implantation. In particular, SSc patients showed dramatic improvement of these parameters (18 of 19 patients, 94.7%). In patients with other types of connective tissue diseases, pain and ulcers improved in 12 of 15 patients (80.0%). No serious adverse event was observed. These results demonstrate that implantation of autologous MNCs from bone marrow or peripheral blood into ischemic digits is feasible, safe and effective for improvement of pain and skin ulcers in patients with connective tissue diseases including SSc. Thus, larger, randomized and controlled trials for this cell therapy in patients with connective tissue diseases will be warranted.