Abstract Conclusion: Risk factors associated with increased carriage rates are the same in children with recurrent acute otitis media (rAOM) as in healthy children. These are also known to be risk factors for the development of AOM itself. Objectives: The aim of this study was to describe risk factors for nasopharyngeal carriage in a cohort of young children at high risk of developing rAOM. Methods: Children with an onset of AOM before 6 months of age, indicating an 80% risk of developing rAOM, were enrolled in a vaccination trial on heptavalent PCV. These children were monitored for 3 years during healthy and AOM periods with nasopharyngeal cultures, physical examinations, and questionnaires. Results: A total of 109 children were included at a mean age of 5 months; 105 were followed for 3 years, 89 (82%) of whom developed rAOM. Risk factors associated with increased carriage of all major AOM pathogens were age <2 years, concurrent AOM, and fulfilment of rAOM criteria. Having siblings in day care was associated with increased carriage of Streptococcus pneumoniae and Haemophilus influenzae, recent antibiotic treatment was associated with H. influenzae and Moraxella catarrhalis carriage, and winter season was associated with M. catarrhalis carriage alone.