Patient registries, frequently referred to as outcome registries, are 'organized systems' that use observational study methods to collect uniform data. Registries are used to evaluate specified outcomes for a population defined by a particular disease, condition or exposure that serves one or more predetermined scientific, clinical or policy purposes. Outcome registries were established very early in the development of hematopoietic SCT (HSCT). Currently, myriads of national and international HSCT registries collect information about HSCT activities and outcomes. These registries have contributed significantly to determining trends, patterns, treatment practices and outcomes. There are many different HSCT registries, each with different aims and goals; some are led by professional organizations, others by government authorities, health care providers or third parties. Some registries simply assess activity and others study outcomes. These registries are complementary and are gradually developing interoperability with each other to expand future collaborative research activities. A key development in the last few years was the incorporation of recommendations into the World Health Organization guiding principles on cell, tissue and organ transplantation. The data collection and analysis should be an integral part of therapy and an obligation rather than a choice for transplant programs. This article examines challenges in ensuring data quality and functions of outcome registries, using HSCT registries as an example. It applies to all HSCT-related data, but is predominantly focused on HSCT registries of professional organizations.