Background: Reliance on hospital discharge diagnosis codes alone will likely underestimate the burden of respiratory viruses. Objectives: To describe the epidemiology of respiratory viruses more accurately, we used record linkage to examine data relating to all children hospitalized in Western Australia between 2000 and 2012. Patients/Methods: We extracted hospital, infectious disease notification and laboratory data of a cohort of children born in Western Australia between 1996 and 2012. Laboratory records of respiratory specimens collected within 48 hours of admission were linked to hospitalization records. We calculated the frequency and rates of virus detection. To identify groups where under-ascertainment for respiratory viruses was greatest, we used logistic regression to determine factors associated with failure to test. Results and conclusions: Nine percentage of 484 992 admissions linked to a laboratory record for respiratory virus testing. While 62% (n = 26 893) of laboratory-confirmed admissions received respiratory infection diagnosis codes, 38% (n = 16 734) had other diagnoses, notably viral infection of unspecified sites. Of those tested, incidence rates were highest for respiratory syncytial virus (247 per 100 000 child-years) followed by parainfluenza (63 per 100 000 child-years). Admissions among older children and those without a respiratory diagnosis were associated with failure to test for respiratory viruses. Linked data can significantly enhance diagnostic codes when estimating the true burden of disease. In contrast to current emphasis on influenza, respiratory syncytial virus and parainfluenza were the most common viral pathogens among hospitalized children. By characterizing those failing to be tested, we can begin to quantify the under-ascertainment of respiratory viruses.