The role of dogs in the transmission of Coxiella burnetii to humans is uncertain, and extensive seroprevalence studies of dogs have not been previously conducted in Australia. This study determined C. burnetii exposure in four diverse canine subpopulations by adapting, verifying and comparing an indirect immunofluoresence assay (IFA) and an enzyme-linked immunosorbent assay (ELISA) used to detect anti-C. burnetii antibodies in humans. Canine serum samples (n = 1223) were tested with IFA from four subpopulations [breeding establishments; household pets; free-roaming dogs in Aboriginal communities; shelter dogs]. The proportions of seropositive dogs were as follows: breeding (7/309, 2.3%), household pets (10/328, 3%), Aboriginal communities (21/321, 6.5%) and shelters (5/265, 1.9%). Dogs from Aboriginal communities were 2.8 times (CI 1.5–5.1; P < 0.001) more likely to be seropositive than dogs from other populations. The ELISA was used on 86 of 1223 sera tested with IFA, and a Cohen's Kappa coefficient of 0.60 (CI 0.43–0.78) indicated good agreement between the two assays. This study has established that Australian dogs within all four subpopulations have been exposed to C. burnetii and that a higher seroprevalence was observed amongst free-roaming dogs associated with Aboriginal communities. As C. burnetii recrudesces during pregnancy and birth products contain the highest concentration of organism, individuals assisting at the time of parturition, those handling pups shortly after birth as well as those residing in the vicinity of whelping dogs are potentially at risk of developing Q fever. However, the identification of active antigen shed in excreta from seropositive dogs is required in order to accurately define and quantify the public health risk.