Autoimmune diseases (ADs) represent a heterogenous group of complex diseases with increasing incidence in Western countries and are a major cause of morbidity. Hematopoietic stem cell transplantation (HSCT) has evolved over the last 25 years as a specific treatment for patients with severe ADs, through eradication of the pathogenic immunologic memory and profound immune renewal. HSCT for ADs is recently facing a unique developmental phase across transplant centers. This review provides a comprehensive overview of the recent evidence and developments in the area, including fundamentals of preclinical research, clinical studies in neurologic, rheumatologic and gastroenterologic diseases, which represent major indications at present, along with evidence of HSCT for rarer indications. Moreover, we describe the interwoven challenges of delivering more advanced cellular therapies, exploiting mesenchymal stem cells, regulatory T cells and potentially CAR-T cell therapies, in patients affected by ADs. Overall, we discuss past and current indications, efficacy, associated risks and benefits, and future directions of HSCT and advanced cellular therapies in the treatment of severe/refractory ADs, integrating the available literature with European Society for Blood and Marrow Transplantation (EBMT) registry data.