An increased relative risk of infection with the 2009 pandemic H1N1 influenza virus associated with pregnancy and Indigenous status has been a common finding in many countries. Using publicly available data from May to October 2009 in Australia, we estimated the relative risk of hospitalisation, admission to intensive care unit and death as 5.2, 6.5 and 1.4 respectively for pregnant women, and as 6.6, 6.2 and 5.2, respectively for Indigenous Australians. Pregnancy and Indigenous status were associated with severe influenza. More complete analyses of risks in these groups are required to understand and prevent influenza morbidity and mortality.