Streptococcus pneumoniae is an important pathogen with significant morbidity and mortality rates worldwide, especially among children <5 years. Healthy carriers are the most important sources of pneumococcal infections, and the nasopharyngeal colonisation is the most prevalent among children attending communities such as day-care centres (DCCs). The conjugate pneumococcal vaccines (PCVs) were shown to have an impact on the colonisation, and so play an important role in inhibiting infections. In this study we compared the nasal carriage of healthy children attending DCCs in Szeged, Hungary in 2003/2004, when nobody was vaccinated, and in 2010, when already 1/5 of the children received PCV-7. Significant differences were observed in the serotype distribution, representing a marked shift from the previously widespread vaccine-types (mostly 6A or 14) to others (11A and 23F). The new serotypes showed higher antibiotic susceptibility. The bacterium exchange between children was clear from the pulsed-field gel electrophoresis (PFGE) patterns, and the circulation of certain international clones plays also a role in these dynamic changes.