Hematopoietic stem cell transplantation (HSCT) is used widely for the treatment of malignant and non-malignant diseases. Advances in transplantation strategies such as modifications to existing transplant-conditioning regimens to lower morbidity and mortality, use of alternative donors and grafts, supportive care including graft-versus-host disease prophylaxis and antimicrobial therapy have led to increasing numbers of HSCT being performed. The procedure is now available to children, young and older adults with an ever increasing number of survivors from this procedure. Analysis of outcomes after HSCT giving consideration to existing strategies warrants using appropriate statistical methodology. This is critical not only in documenting the current success of HSCT but to plan future strategies to optimize accessibility to HSCT, donor and graft choices, patient selection, counsel potential HSCT candidates and long-term survivors and plan intervention trials for these persons. We describe concepts and principles of HSCT to better understand the complexities associated with outcome analysis.