The 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) and the 13-valent pneumococcal conjugate vaccine (PCV13) replaced the 7-valent PCV (PCV7) in May 2010 in Korea. We investigated the dynamics of pneumococcal nasopharyngeal (NP) colonization in children with a respiratory illness before and after use of PHiD-CV and PCV13.From March 2009 to December 2012 NP secretions were obtained from 2176 children aged < 5 years with respiratory diseases. We used the multiplex polymerase chain reaction (PCR) technique to determine pneumococcal serotypes.Among the samples, 468 (21.5%) specimens were positive by multiplex PCR. The overall pneumococcal colonization rate remained stable during the 2009-2012 periods. The serotypes present in PCV7 and serotype 19A decreased in frequency from 36.8% and 26.4% in 2009 to 10.1% and 11.4% in 2012, respectively (χ(2) for trend, P < 0.001 and P = 0.007, respectively). The frequency of non-PCV13 serotypes increased from 36.8% in 2009 to 78.5% in 2012 (χ(2) for trend, P < 0.001). There was no significant difference in carriage rates of each serotype between groups of children that received PCV7, PHiD-CV, or PCV13.Compared with the period of PCV7 vaccination, overall carriage rate was not affected by the introduction of new PCVs. However, serotype distribution now consists mostly of non-vaccine serotypes. PCVs affect mucosal immunity against Streptococcus pneumoniae (SP) in NP carriage; but, global SP colonization seems to be maintained by replacement.