Q fever (infection with Coxiella burnetii) has been uncommon in Australia's Northern Territory, with no reported cases until 2002. Since then, twelve cases of Q fever have been reported, representing a much lower notification rate than in surrounding Australian states. Three cases were identified in Central Australia during 2006, prompting this review of clinical and epidemiological features of all notified Northern Territory cases. Three patients required Intensive Care admission, 1 died, 5 had moderately severe illness, 2 were treated as outpatients and 2 were excluded as unlikely Q fever cases on clinical grounds. Hospital stays were long (median length of stay 9.5 days), and diagnosis and definitive therapy were generally delayed. Although macrolides and quinolones have some reported efficacy against C. burnetii, 2 patients experienced prolonged fever (5 and 9 days respectively) despite azithromycin, and the fatality occurred in a patient treated with multiple antibiotics including ciprofloxacin. Four patients were Aboriginal, 3 were tested for HTLV-1 and 2 were positive. The patient who died was diabetic. None of acute and chronic manifestations of Q fever is required in the Northern Territory. Early institution of doxycyline in suspected cases is recommended, and more rapid diagnostic methods including polymerase chain reaction testing should be considered. Host risk factors for chronicity, which may be of particular importance in Indigenous patients, merit attention. Given the lack of occupational exposure in these cases, there seems little reason to change the current Northern Territory policy of opting out of the National Q Fever Vaccination Program. Recognised alternative exposures, such as non-occupational livestock and domestic animal contact, require consideration as local Q fever sources.