Viral respiratory infections are common in infants and can be severe. The new pandemic influenza virus H1N1v2009 was feared to cause particularly severe outcomes. This study aimed at evaluating the impact of H1N1v2009 on the viral epidemiology, the clinical presentation and the severity of respiratory infections in infants. This prospective epidemiologic study included all infants <2 years of age, both inpatients and outpatients, presenting with respiratory symptoms, from November 2009 through April 2010, at the pediatric emergency department of the University Hospital of Caen, France. A nasal swab was taken for viral detection and analyzed by immunofluorescence and, if negative, polymerase chain reaction. Severe respiratory infection was defined by a score of respiratory severity. One thousand twenty-one infectious episodes with a respiratory sample met inclusion criteria. Eight hundred thirty-four samples (81.7%) were positive. The viruses with the highest incidence were the respiratory syncytial virus (34.2%), the rhinoviruses (23.9%), the coronaviruses (9.3%) and H1N1v2009 (7.7%). Of all infections, 28.6% were severe and more frequent in infants with risk factors. H1N1v2009 infections had a low risk of severe respiratory disease (odds ratios = 0.15) and hospitalization (odds ratios = 0.40) compared with the other viruses. Respiratory syncytial virus infections had a high risk of respiratory severity (odds ratios = 7.85) and were responsible for 71.4% of admissions to the intensive care unit. Despite the modest impact of H1N1v2009 observed in this study, further surveillance is needed to detect virological factors that may increase its severity.