Human rhinoviruses (HRV), enteroviruses (HEV) and parechoviruses (HPeV) have been linked to acute otitis media (AOM). We evaluated this association in a prospective birth cohort setting.324 healthy infants were followed up from birth to the age of 3 years. Nasal swab samples were collected at the age of 3, 6, 12, 18, 24, and 36 months, and screened for HRV and HEV using real-time RT-qPCR. Stool samples were collected monthly and analyzed for HRV, HEV and HPeV. AOM episodes diagnosed by physician were reported by parents in a diary. The association of viruses with AOM was analyzed using Generalized Estimation Equation and their relative contributions using population attributable risk per cent (PAR%).A clear association was found between AOM episodes and simultaneous detection of HEV (adjusted Odds Ratio (aOR) for the detection of virus in stools 2.04, 95% CI 1.06-3.91) and HRV (aOR 1.54, 95% CI 1.04-2.30). HPeV showed a similar, yet non-significant trend (aOR 1.44, 95% CI 0.81-2.56). HRV and HEV showed higher PAR% (25% and 20%) than HPeV (11%).HEVs and HRVs may contribute to the development of AOM in a relatively large proportion of cases.