The parasite Cryptosporidium spp. causes gastroenteritis. Transmission to humans occurs via contaminated water and food, and contact with infected animals and people. To identify high risk populations and potential risk factors for this disease in Australian populations, we analysed long-term cryptosporidiosis patterns across Australia (2001-2012) and reviewed published Australian studies including jurisdictional health bulletins. Spatial analyses showed that rates of reported cryptosporidiosis were highest in the warmer, remote regions and in Aboriginal and Torres Strait Islander populations. Our review of 34 published studies and seven health department reports on cryptosporidiosis in Australia highlighted a lack of long term, non-outbreak studies in these regions and populations, with an emphasis on outbreaks and risk factors in urban areas. Of note, the Incidence Risk Ratio (IRR) of reported cryptosporidiosis in children <5 years was higher in inner regional (IRR 1.4 95% CI 1.2–1.7, p < 0.001), and outer regional areas (IRR 2.4 95% CI 2.2–2.9, p < 0.001), and in remote (IRR 5.2 95% CI 4.3–6.2, p < 0.001) and very remote (IRR 8.2 95% CI 6.9–9.8, p < 0.001) areas, compared to major cities. A linear test for trend showed a statistically significant trend with increasing remoteness. Remote communities need to be a priority for future targeted health promotion and disease prevention interventions to reduce cryptosporidiosis in these vulnerable populations.