The disease burden attributable to influenza is difficult to determine, as influenza infections are rarely virologically confirmed or recorded. Estimating the influenza-related disease burden is a prerequisite to estimate the costs. Age-specific regression models were used to estimate the number of excess hospitalisations attributable to influenza from influenza and respiratory syncytial virus surveillance data. The number of general practitioner consultations for influenza/influenza-like illness was estimated from a continuous randomly sampled national study of general practice activity. Utilising the associated costs for each of these events, a cost-of-illness study was developed from the perspective of the Australian healthcare system. There was an annual average of 310,000 general practitioner consultations for influenza/influenza-like illness and 18,400 hospitalisations attributable to influenza over the period of review. The estimated cost to the Australian healthcare system for these events was $115 million annually. Influenza-related disease places a significant financial burden on the Australian healthcare system.