Acute otitis media (AOM) is the leading bacterial infection in childhood and the main reason for antibiotic prescriptions in children. The success of pneumococcal conjugate vaccines (PCVs) in reducing invasive pneumococcal disease has been demonstrated in many studies. Because Streptococcus pneumoniae is one of the two main bacterial species implicated in AOM, the incidence and characteristics of AOM might also be modified by PCVs. Pre-licensure controlled studies showed that the effect was modest. However, after PCV7 implementation, the impact on the AOM burden appeared to be more marked, despite the fact that serotype replacement in the nasopharynx was almost complete. Most data on the impact of PCVs on nasopharyngeal flora have been drawn from studies with PCV7. No difference was observed with PCV10 compared with PCV7 concerning S. pneumoniae and Haemophilus influenza carriage. For PCV13 compared with PCV7, additional reduction of carriage of serotypes 1, 6A, 7F, 6C, 19A, and 19F was observed, but for the other serotypes, the two PCVs seemed to have the same effect.