Allogeneic hematopoietic stem cell transplantation (HSCT) is indicated in various nonmalignant disorders that arise from genetic, hematopoietic, and immune system defects. Many of the disorders described here have life-threatening consequences in the absence of HSCT, a curative intervention. However, timing and approach to HSCT vary by disorder and optimum results are achieved by performing transplantation before irreversible disease-related morbidity or infectious complications. This article details the principles of HSCT in the very young, lists indications, and explores the factors that contribute to successful outcomes based on transplantation and disease-related nuances. It provides an overview into the HSCT realm from a neonatologist’s perspective, describes the current status of transplantation for relevant disorders of infancy, and provides a glimpse into future efforts at improving on current success.