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All Streptococcus pneumoniae disease is preceded by nasopharyngeal (NP) colonization. We studied the impact of 7-valent pneumococcal conjugate vaccine (PCV7) on colonization in healthy children.Routine PCV7 vaccination began in Alberta in 2002. Six point prevalence surveys were conducted from 2003 to 2005, in 7 community health centers in Calgary where children had their routine vaccinations. A questionnaire was administered and a single NP swab was obtained for culture. Serotyping was performed on all S. pneumoniae isolates.There were 3398 children with complete data, 1307, 1225, and 866 in 12-month, 18-month, and 4–6 year groups, respectively. None had received PCV7 in survey 1. From survey 2 onwards, 92–98% of 12-month-olds had 3 or more doses of PCV7, and from survey 3 onwards, 95–99% of 18-month-olds had 3 or more doses. By survey 6, only 4% of 4–6 year olds had 3 or more doses. The overall S. pneumoniae colonization rate was 20%. In all age groups, including unvaccinated 4–6 year olds, there were significant declines in PCV7 serotypes, and increases in non-PCV7 serotypes. The largest increases were serotypes 6A, 15C, and 11A. Multivariate analysis found that factors including age, siblings, daycare attendance, episodes of otitis media, and antibiotic use affected S. pneumoniae colonization but only PCV7 vaccination was associated with decreased PCV7 serotype colonization and increased non-PCV7 colonization.Routine PCV7 vaccination has led to significant changes in the predominant S. pneumoniae serotypes found in NP colonization in both vaccinated and unvaccinated children, indicating both a direct and herd effect.