OBJECTIVES: To evaluate the cost effectiveness of ‘sore throat clinics’ (STCs) for prevention of acute rheumatic fever (ARF) in children in primary/intermediate schools. METHODS: A Markov model was developed to represent the lifetime impact of one year of primary prevention of ARF with STCs in high risk New Zealand (NZ) schools. It includes the incidence rate, natural history and costs of ARF and rheumatic heart disease; secondary prophylaxis; medical management of carditis; cardiac valve repair/replacement; the overall efficacy of community interventions to prevent rheumatic fever; and the annual cost per child of STCs. The model has a cycle of one year and terminates at age 95. It takes a healthcare payer perspective but excludes costs to families. Future costs and health benefits are discounted at 3.5% per annum. RESULTS: If STCs are 59% efficacious and cost on average NZ$135 per child per year, for schools at an incidence rate of 75 per 100,000, STCs can be expected to cost about NZ$60,000 per QALY gained or NZ$190,000 per ARF case averted or NZ$2m per death averted. These figures are sensitive to the efficacy and annual cost of the intervention and the incidence of ARF but robust to uncertainty in other variables. The main costs are for project workers and laboratory culture and the main uncertainty is the efficacy of the intervention in NZ high risk schools. CONCLUSIONS: Sore throat clinics in high risk schools are likely to reduce the risk of acute rheumatic fever and thereby improve survival of Mâori and Pacific children, although they appear to be poorly cost effective from a NZ government perspective. Their cost effectiveness could be improved by containing staffing costs and/or reducing the cost of laboratory diagnosis of GAS. Implementation of this intervention would reduce the striking disparity between Mâori/Pacific and others.