We performed a cost-utility analysis for various vaccination strategies against meningococcal and pneumococcal diseases (MenC or MenC/PCV-9) in Switzerland. The analysis compared the current recommendations of vaccinating only children with medical risks to the introduction of the vaccination with either the MenC or the MenC/PCV-9 vaccine, administered at 12 or 2, 4 and 6 months of age, into the existing immunisation programme. For a birth cohort of 80,000 children and assuming a vaccine coverage of 80%, the introduction of a generalised vaccination would be cost-effective. The strategy using three doses of MenC/PCV-9 would achieve the highest health benefit, with 440 quality-adjusted life years (QALYs) gained at costs of 34,000 per QALY.