BACKGROUND: Reliable epidemiologic surveillance of infectious diseases is important for making rational choices for public health issues such as vaccination strategies. In Belgium, as in most European countries, surveillance relies on voluntary passive reporting from microbiology laboratories; therefore, reported incidence rates are probably inaccurate. METHODS: We conducted national, active, laboratory-based and clinically based surveillance of invasive pneumococcal disease in young children. RESULTS: During the study period, the incidences of invasive pneumococcal disease in children < 2 years of age (104.4 cases per 10(5) person-years and 16.1 cases per 10(5) person-years for invasive pneumococcal disease and meningitis, respectively) and in children 0 to 59 months of age (59.5 cases per 10(5) person-years for invasive pneumococcal disease and 7.7 cases per 10(5) person-years for meningitis) were twice those reported previously through the passive surveillance system. Overall, 67% of the Streptococcus pneumoniae strains isolated from children < 5 years of age belonged to 7-valent pneumococcal conjugate vaccine serotypes and 18% to vaccine-related serotypes (mainly serotype 19A). Erythromycin resistance was frequent, especially among children < 2 years of age (59%). CONCLUSIONS: Under-reporting can explain the reported low incidence of invasive pneumococcal disease in countries (such as Belgium) that depend on a passive epidemiologic surveillance system, which could lead to erroneous choices in vaccination policies. There is a need for an active system of epidemiologic surveillance for vaccine-preventable diseases such as invasive pneumococcal disease, at the national or European level.