T-regulatory disorders are a heterogenous group characterized by autoimmune and allergic manifestations of varying onset, severity, and progression. The advent of sophisticated molecular and immunologic diagnostic techniques has resulted in accurate elucidation of etiopathogenesis of many immunoregulatory disorders previously clubbed under the autoimmune umbrella. The severity of presentation and progression, early morbidity and mortality, poor quality of life, and frequent refractoriness to immunosuppressive therapy has prompted studies of stem cell transplantation in many immunoregulatory disorders. The benefits of autologous or allogeneic transplantation are related to either suppression and reprogramming of the immune system (autologous transplant) or replacement of missing elements of immune regulation (allogeneic transplants). Transplant methods have steadily improved through a series of studies and trials to have the benefits of this approach outweigh the risks of procedure-related toxicities. This article summarizes the current status and the future goals of stem cell transplantation for T-cell immunoregulatory disorders and reviews advances in disease detection, targeted transplant strategies and novel approaches, and the pros and cons of transplant in this field.