Health and economic burden of recurrent respiratory tract infections (RTIs) in early childhood is considerable. A systematic review of licensed influenza and pneumococcal vaccines showed substantial efficacy in children, but the health-economic impact of such vaccines among pre-school children with recurrent RTIs is unknown. We therefore, designed a double-blind randomized controlled trial to determine the effectiveness and costs of a combined influenza and pneumococcal vaccination program among a primary care based cohort of children with recurrent episodes of RTI aged between 18 and 72 months. We will enroll 690 children over three consecutive years (2003--2005) who will be randomly allocated to receive vaccinations against influenza and pneumococcal disease, influenza alone or hepatitis B in a similar schedule. Follow up by parental diaries, tympanic temperature measurements, questionnaires and interviews is planned until May 2006. Primary outcome is number of febrile RTIs. Other outcomes include duration and severity of RTI episodes, medical consumption, safety and costs.