In Australia, little is known about how the incidence rate (IR) of lower limb amputation (LLA) varies across the country. While studies in other economically developed countries have shown considerable geographic variation in the IR-LLA, mostly these have not considered whether the effect of common risk factors are the same across regions. Mapping variation of the IR-LLA, and the effect of common risk factors, is an important first step to focus research into areas of greatest need and support the development of regional specific hypotheses for in-depth examination. The aim of this study was to describe the geographic variation in the IR-LLA across Australia and understand whether the effect of common risk factors was the same across regions. Using hospital episode data from the Australian National Hospital Morbidity database and Australian Bureau of Statistics, the all-cause crude and age-standardised IR-LLA in males and females were calculated for the nation and each state and territory. Generalised Linear Models were developed to understand which factors influenced geographic variation in the crude IR-LLA. While the crude and age-standardised IR-LLA in males and females were similar in most states and territories, they were higher in the Northern Territory. The effect of older age, being male and the presence of type 2 diabetes was associated with an increase of IR-LLA in most states and territories. In the Northern Territory, the younger age at amputation confounded the effect of sex and type 2 diabetes. There are likely to be many factors not included in this investigation, such as Indigenous status, that may explain part of the variation in the IR-LLA not captured in our models. Further research is needed to identify regional- and population- specific factors that could be modified to reduce the IR-LLA in all states and territories of Australia.