OBJECTIVES: Factor concentrates composed of human blood plasma carry the risk of transmitting blood-borne pathogens. This study evaluated health and economic consequences of infection in haemophilia A patients in the event of a novel pathogen emerging that can be transmitted through blood products. METHODS: A decision analytic model was constructed to explore consequences and costs of new pathogen emergence. The population considered was all patients with haemophilia A requiring Factor VIII prophylaxis in Sweden. The annual risk of a new pathogen emerging was estimated as the average rate of new agent emergence reported by the World Health Organisation. The percentage of the population likely to be infected was varied reflecting uncertainty around reduced use of human proteins in newer factor VIII products. The impact of resulting infections on length and quality of life was estimated using quality adjusted life years, taking mean values for historical infections as a base case. RESULTS: Over 20 years the World Health Organisation reported 30 newly identified diseases, of which 5 were transmissible by transfusion. The annual risk that a new blood-born pathogen will emerge was estimated to be 16.7%.  If 5% of patients were infected economic loss would be 0.05 QALYs and €6000 per patient. If all patients were infected the economic loss was estimated to exceed €100,000 and 1.06 QALYs per patient treated. Over 80% of the economic loss is reduced productivity. The model findings are sensitive to the expected rate of new pathogen emergence. CONCLUSIONS: New blood-born pathogens emerge frequently. The model estimated that the health and economic consequences of transmission of a new pathogen may be severe.  Even at low levels of infection risk, measures to further reduce the likely percentage of individuals infected by any new agent will have health and economic benefits.