Malaria is a notifiable disease in Australia with an average of 600 notifications per year in returned travellers or newly arrived refugees, migrants and visitors. Although endemic disease has been eliminated from the tropical north of Australia, the region remains malaria receptive due to the presence of efficient mosquito vectors. This study analyses enhanced surveillance data collected by the Centre for Disease Control on all cases of malaria notified in the Northern Territory from 1 January 2000 to 31 December 2010. There were 428 malaria episodes notified that occurred in 391 individuals with a median age of 26 years. Of these, 71.4% were male, 40.5% were Australian nationals and 38.0% were prescribed chemoprophylaxis. Primary infection consisted of 196 (51.3%) cases of Plasmodium falciparum, 165 (43.2%) P. vivax, 2 (0.5%) P. ovale, 1 (0.3%) P. malariae and 18 were mixed infections. There were 46 episodes of relapsed infection. Residents of non-malarious countries were most likely to have acquired primary infection in East Timor (40.6%), Papua New Guinea (27.8%), Indonesia (18.7%) and Africa (6.4%). Primary infection was diagnosed after a median 19 days (interquartile range (IQR) 7-69) after arrival in Australia for cases of P. vivax compared with 4 days for P. falciparum (IQR 2-11). Screening protocols led to the diagnosis of 27.2% of cases. Eighty-seven per cent of patients were admitted to hospital at the time of their malaria diagnosis with median duration of 3 days (IQR 2-4) and one patient died. Resettlement of people from endemic countries, as well as military and civilian activities, influences the prevailing notification rates and Plasmodium species type.