Factor IX (FIX) inhibitors develop in 1·5–3% of haemophilia B patients. Due to its low incidence compared with that in haemophilia A, few comparable data exist on host and treatment-related risk factors, and immunological processes associated with FIX inhibitor development. Moreover, the safety and efficacy of bypass therapy as well as the outcome predictors of successful inhibitor eradication have been poorly characterised. The lack of a useful evidence-based approach to the diagnosis and management of FIX inhibitors complicates their significant morbidity due to the frequency of allergic reactions that often herald antibody development. This review discusses what is currently known about the epidemiology, natural history and immunology of anti-FIX antibody development. It addresses several special considerations in the approach to the treatment of bleeding and inhibitor eradication. A case is made for moving forward with an integrated international collaboration for the further study of the nature and treatment of this problem.