OBJECTIVE: Until 2001 serotype prevalence of meningococcal disease in Portugal was unknown. Following the first release of data it was found that a high prevalence of type C disease existed in Portugal (>50% all serotypes). Several conjugated vaccines are currently available, all having several possible vaccination schemes. This study estimates the cost-effectiveness of two different vaccination schemes using the vaccine MeningiteC(r). METHODS: Using an Excel-based model we estimated the impact of vaccinating 100,000 children, using alternatively 2 different vaccination schemes (1 vs 3 doses). Disease prevalence was assumed as the one found during the year previous to the introduction of the vaccine. The vaccine was assumed as having a 92% efficacy for 5 years, with no herd immunity. Costs were obtained from official sources, when available. The estimation of resources for disease and sequelae treatment was obtained by consulting several clinical experts. Costs were determined in 2002 Euros and a discount rate of 5% was used, as required by Portuguese guidelines. RESULTS: For each 100.000 children vaccinated, using a 3-dose scheme will result in 345,36 Life-Years Gained (LYG), with cost-effectiveness ratios of €29.575/LYG - societal, and €11.272/LYG - 3rd payer, while the vaccination with only one dose will result in 297,58 LYG, with ratios of €10.806/LYG and €3.768/LYG, respectively. The results found are sensitive to vaccine price, epidemiology of disease and mortality rates. Resources consumed due to disease and sequelae did not influence final results considerably. CONCLUSION: Use of meningococcal C vaccine in Portugal is expected to be cost-effective provided that no substantial change in the prevalence of the disease occurs. Decision to use 1 or 3 doses will depend on both society's and parent's willingness to pay since incremental cost-effectiveness ratios for the 3 vs 1 dose scheme are considerably high.