A key challenge for evaluators and health system planners is the identification, measurement and valuation of resource use for economic evaluation. Accurately capturing all significant resource use is particularly difficult in the Australian context where there is no comprehensive database from which researchers can draw. Evaluators and health system planners need to consider different approaches to data collection for estimating resource use for economic evaluation, and the relative merits of the different data sources available. This paper illustrates the issues that arise in using different data sources using a sub-sample of the data being collected for an economic evaluation. Specifically, it compares the use of Australia's largest administrative database on resource use, the Health Insurance Commission database, with the use of patient-supplied data. The extent of agreement and discrepancies between the two data sources is investigated. Findings from this study and recommendations as to how to deal with different data sources are presented.