BACKGROUND Pneumococcal conjugate vaccine, 7 valent (PCV7) is the most costly vaccine yet considered for publicly funded programs. In mid 2001, Australia funded PCV7 for high-risk groups only (indigenous children and children with certain underlying medical conditions). World wide, non-industry-funded studies and studies using cost-utility measures are sparse. We undertook an independent economic analysis of PCV7 compared with no vaccination in the non high-risk Australian childhood population using cost-utility and cost-effectiveness measures. METHODS The incidence of invasive pneumococcal disease (IPD), non-bacteraemic pneumonia and otitis media was estimated using representative urban Australian data, or by extrapolation from comparable industrialised countries. A decision-analytic model was developed for a hypothetical birth cohort using the age-specific vaccine coverage from the Californian randomised controlled trial of PCV7. Health outcomes were measured by life-years saved and deaths and disability-adjusted life-years (DALYs) averted. In line with government guidelines, only direct costs were considered in 1997-1998 Australian dollars. RESULTS For a birth cohort of 250,000, the gross cost of vaccination is $ 78.6 million. Subtracting treatment cost savings, the net cost (discounted) is $ 61.7 million. In undiscounted terms, vaccination prevents 13.7 deaths, 11.2 (82%) from IPD and the remainder from non-bacteraemic pneumonia. The discounted cost per death avoided is $ 5.0 million, per life-year saved $ 230,130 and per DALY averted $ 121,100, giving a break-even vaccine price of $ 15.40 per dose. These estimates are most sensitive to the unit cost per dose of vaccine, estimates of incidence and vaccine efficacy against non-bacteraemic pneumonia and the discount rate. The cost per DALY reduced to $ 81,000 with a discount rate of 3% rather than 5% and to $ 90,000 with the most favourable assumptions concerning pneumonia reduction. CONCLUSIONS With a vaccine price of $ 90 per dose, mid-range estimates of impact against non-bacteraemic pneumonia, and discount rate of 5%, a PCV7 program for infants not at high risk of IPD is at the upper limit of cost per DALY previously approved under Australian pharmaceutical funding guidelines. The impact of PCV7 against non-bacteraemic pneumonia is poorly defined, but its importance to cost-effectiveness in resource rich and resource poor settings warrants further studies or analysis to give greater precision to this outcome.