Background Long term illness has far reaching impacts on individuals, and also places a large burden upon government. This paper quantifies the indirect economic impacts of illness related early retirement on individuals and government in Australia in 2009. Methods The output data from a microsimulation model, Health&WealthMOD, was analysed. Health&WealthMOD is representative of the 45 to 64 year old Australian population in 2009. The average weekly total income, total government support payments, and total taxation revenue paid, for individuals who are employment full-time, employed part-time and not in the labour force due to ill health was quantified. Results It was found that persons out of the labour force due to illness had significantly lower incomes ($218 per week as opposed to $1167 per week for those employed full-time), received significantly higher transfer payments, and paid significantly less tax than those employed full-time or part-time. This results in an annual national loss of income of over $17 billion, an annual national increase of $1.5 billion in spending on government support payments, and an annual loss of $2.1 billion in taxation revenue. Conclusions Illness related early retirement has significant economic impacts on both the individual and on governments as a result of lost income, lost taxation revenue and increased government support payments. This paper has quantified the extent of these impacts for Australia.