The World Health Organization recommends vaccination of pregnant women for seasonal influenza that can also protect infants aged below 6 months. We estimated incidence and disease burden of influenza in hospitalised children below and above 6 months of age in Hong Kong during a 6 year period. Discharge diagnoses for all admissions to public Hong Kong Hospital Authority hospitals, recorded in a central computerised database (Clinical Management System, CMS), were analysed for the period April 2005 to March 2011. Incidence estimates of influenza disease by age group were derived from CMS ICD codes 487-487.99. Laboratory-confirmed influenza infections from a single surveillance hospital were then linked to the CMS entries to assess possible over- and under-diagnosis of influenza based on CMS codes alone. Influenza was recorded as any primary or any secondary diagnosis in 1.3% (1158/86,582) of infants aged above 6 days to below 6 months and 4.3% (20,230/471,482) of children above 6 days to below 18 years. The unadjusted incidence rates per 100,000 person-years based on any CMS diagnosis of influenza in all admission to Hong Kong public hospitals were 627 in the below 2 months of age group and 1762 in the 2 month to below 6 month group. Incidence of hospitalisation for influenza in children was highest from 2 months to below 6 months. In the absence of vaccines for children below 6 months of age, effective vaccination of pregnant women may have a significant impact on reducing influenza hospitalisations in this age group.