There is no current information regarding the prevalence of hookworm in Australian dogs and cats and based on the results of studies conducted over 20 years ago, where high prevalences of helminths were recorded, the prophylactic administration of broad spectrum anthelmintics has been advocated. During this study, faecal samples were collected from dogs (n=1391) and cats (n=1027) across Australia. Samples were examined by microscopy and information regarding the demographics of each animal, and the management practices they experienced were recorded. A highly sensitive and species-specific PCR-RFLP technique was utilized to differentiate the various hookworm species which can infect dogs and cats directly from eggs in faeces. The prevalence of hookworm in dogs and cats was found to be 6.9% and 1.4%, respectively. Ancylostoma ceylanicum was detected for the first time in Australia in 10.9% of the dogs found positive for hookworm. Significantly, A. ceylanicum is capable of causing a patent infection in humans. After adjusting for other factors with multiple logistic regression, dogs from refuges, dogs originating from a tropical climatic zone, dogs aged 1 year or less, and those dogs which had not received anthelmintics were significantly more likely to be parasitized. Only univariate analysis was conducted for the cats as there were too few samples positive for hookworm. Cats were more likely to be infected with hookworm if they were from refuges, originated from a tropical climatic zone, and had not received treatment with anthelmintics. The results of this study demonstrates the importance of having current information regarding the prevalence of parasites of dogs and cats and the risk factors associated with infection, as well as the need to reassess the veterinary and public health concerns regarding hookworm infection and its control, which are currently based on out-dated information.