Aim This article seeks to highlight the methodological issues involved in the public health economics of vaccines in the Netherlands and the ensuing implications for immunisation policy. Subjects and methods We review and analyse the role of health economics (and especially cost-effectiveness issues) in the decision-making process of the Dutch (1) Drugs Reimbursement System and (2) National Immunisation Programme. Different types of health-economic analyses are illustrated by the examples of meningococcal C, pneumococcal, and human papilloma virus (HPV) vaccines. Results The role of health economics has recently increased in importance in Dutch public health decision-making concerning vaccines. The choice of vaccine strategy against meningococcus C, the shift in favour of introducing pneumococcal vaccine, and the prolonged decision on the reimbursement for HPV vaccine were all related to the health-economic component in the recommendation process. Conclusion The role of health economics is growing in decision-making regarding the reimbursement of new therapeutic and prophylactic products. Vaccines, like drugs, will have increasingly to prove their cost-effectiveness if manufacturers are to lead their product not only from phases I to IV, but also through to implementation as part of national immunisation policies covered within national reimbursement systems.