Vasculopathy in patients with connective tissue diseases (CTDs), including systemic sclerosis (SSc) and systemic lupus erythematosus (SLE), is a serious complication that mainly affects small arteries and capillaries, reduces the blood flow and causes progressive tissue ischemia. Recently, CTD patients have been reported to have abnormalities in circulating endothelial progenitor cells (EPCs); these abnormalities are believed to contribute to the pathophysiology of vasculopathy and to the premature and accelerated development of atherosclerosis in CTD patients. Furthermore, we are currently conducting a clinical pilot study to determine the efficacy of implanting autologous mononuclear cells obtained from the bone marrow and peripheral blood into the ischemic digits or limbs of CTD patients. In this review, we discuss the role of EPCs in the process of neovascularization and in the pathophysiology of CTDs, and we describe a clinical pilot study on the use of autologous cell therapy for treating ischemic digits in patients with CTDs.