The design and conduct of clinical trials of haematopoietic stem cell transplantation (HSCT) for autoimmune diseases requires investigators to address issues unique to this therapeutic approach and patient population. The proper composition of the protocol team is central to success. It is important to recognize that transplant physicians are no longer also the disease experts when transplanting patients with autoimmune diseases, and a close collaborative relationship between these groups early in the design stage must continue through the care of patients on trial to the assessment of toxicity and response. The early involvement of statisticians expert in clinical trial design and patient representatives are also vital to developing the optimal protocol. Each step in design and implementation requires particular consideration of the unique aspects of applying HSCT to autoimmune diseases. Some areas discussed are the role of disease and transplant databases in designing and analysing clinical trials, design options for early-phase trials, maintaining clinical equipoise, eligibility criteria, blinding, outcome measures and statistical analysis, and the composition and role of the data safety and monitoring boards. Although no blueprint for designing and conducting a trial of HSCT for autoimmune diseases can be laid out, the process should take into consideration the issues highlighted herein.