BACKGROUND: The effect of the 2009 H1N1 influenza pandemic on viral epidemiology of upper and lower respiratory tract infections (URI and LRI) in healthy infants in the first year of life has not been well studied. METHODS: A total of 180 healthy infants were enrolled from birth and monitored for occurrences of URI, LRI and acute otitis media complications until the first acute otitis media episode or between 6 and 12 months of age. Nasopharyngeal specimens collected during acute respiratory illnesses were tested for 18 viruses. RESULTS: Between October 2008 and April 2011, 373 URI episodes, including 20 with LRI, in 139 infants were documented. Viral studies were performed on 189 URI episodes; 87% were positive. Throughout the 31-month period (1386 patient-months), rhinovirus was the predominant virus causing URI (55%); respiratory syncytial virus was the major cause of LRI (64%). Although there was a significant increase in parent-initiated visit rate during the 15-month influenza pandemic as compared with prepandemic and postpandemic periods, only 4 cases of influenza were detected (2 cases during and 2 cases prepandemic and postpandemic). CONCLUSIONS: The 2009 influenza A/H1N1 pandemic had no impact on the overall viral epidemiology of respiratory infections in healthy infants in the first year of life but resulted in increased parent-initiated visits due to respiratory symptoms. Maternal antibody and absence of comorbidity may explain the low influenza burden whereas parental anxiety may explain the increased healthcare visit rate during the pandemic.