To make a direct comparison between the total burden of pandemic influenza and that of other seasonal influenza A viral subtypes in otherwise healthy children.The total clinical and socioeconomic burden of pandemic A/H1N1/2009 influenza was compared with that of seasonal influenza A viral subtypes in 389 otherwise healthy children with A/H1N1/2009, 126 with seasonal A/H1N1 and 486 with seasonal A/H3N2 infection referred to the Emergency Room and hospitalised in the in-patient units of a large, university-based paediatric hospital. Influenza diagnosis was confirmed by real-time polymerase chain reaction.Regardless of age or gender, the variables significantly associated with pandemic A/H1N1/2009 and seasonal A/H3N2 infection were a diagnosis of lower respiratory tract infection upon clinical presentation, the need for hospitalisation, hospitalisation for ≥7 days, school absences of ≥7 days, the need for aerosol therapy, the household development of a disease similar to that of the infected child, and the need for additional household medical visits and antibiotic prescriptions (p < 0.001). A longer period of hospitalisation and lost school days seemed to be associated with pandemic A/H1N1/2009 infection (p < 0.01).Perceived symptom severity and the risk of serious outcomes are similar in children with influenza due to pandemic A/H1N1/2009 or seasonal A/H3N2 influenza, but both of these viruses seem to have a greater clinical and socioeconomic impact than seasonal A/H1N1 virus, regardless of the patients’ age or gender.