Objectives: To explore National Health and Medical Research Council (NHMRC) funding for each National Health Priority Area (NHPA) over time and by grant type, and to quantify the relationship between grants awarded and a range of measures of societal burden of disease (BoD). Design and setting: We conducted a retrospective analysis of NHMRC funding for each NHPA from 2000 to 2008 to assess the strength of correlation between level of NHMRC funding and contribution of each health condition to BoD. Information on mortality, incidence, prevalence, “healthy” years of life lost due to disability (YLD), years of life lost due to premature mortality (YLL) and disability-adjusted life-years (DALYs) was obtained from the 2003 Australian BoD study. Information on health system expenditure for each NHPA was obtained from an Australian Institute of Health and Welfare report. Main outcome measures: Observed versus expected number of grants; amount of funding allocated to each NHPA; relative contribution of each NHPA health condition to BoD. Results: 6099 new and continuing NHMRC grants were linked to NHPAs. Total NHMRC funding by NHPA was strongly correlated with YLL and DALYs, but there was no clear association between the amount of funding per NHPA and YLD or health system expenditure. Based on the proportional contribution of each NHPA health condition to total NHPA-related DALYs, a higher than expected number of grants was allocated to diabetes and cancer research, and a lower than expected number to injury and mental health research. Conclusions: Some of Australia’s NHPAs are better funded than others. The NHMRC could begin to redress this imbalance by allocating research and workforce development funding to less well developed research areas to ensure appropriate resourcing that is commensurate with their contribution to BoD.