During a 5-year prospective study of nasopharyngeal (NP) colonization and acute otitis media (AOM) infections in children during the 7-valent pneumococcal conjugate vaccine (PCV) era (July 2006–June 2011) we studied risk factors for NP colonization and AOM. NP samples were collected at ages 6, 9, 12, 15, 18, 24, and 30 months during well-child visits. Additionally, NP and middle ear fluid (MEF) samples were collected at onset of every AOM episode. From 1825 visits (n = 464 children), 5301 NP and 570 MEF samples were collected and analysed for potential otopathogens. Daycare attendance, NP colonization by Moraxella catarrhalis, and siblings aged <5 years increased the risk of Streptococcus pneumoniae NP colonization. NP colonization with S. pneumoniae, M. catarrhalis, or Haemophilus influenzae and a family history of OM increased the risk of AOM. Risk factors that increase the risk of pneumococcal AOM will be important to reassess as we move into a new 13-valent PCV era, especially co-colonization with other potential otopathogens.