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Worldwide, foodborne illness is a significant public health issue in both developed and developing countries. Salmonellosis, campylobacteriosis and shigellosis are common foodborne gastrointestinal illnesses caused by the bacteria Salmonella spp., Campylobacter spp. and Shigella spp. respectively. These zoonotic diseases are frequently linked to eggs and poultry products. The aim of this study was to investigate the presence of these pathogens in Australian backyard poultry flocks and to determine risk factors for these pathogens. Poultry faeces samples were collected from 82 backyards and screened for Salmonella spp., Campylobacter spp. and Shigella spp. using qPCR. A questionnaire was administered to the backyard poultry owners to assess their knowledge regarding management of poultry and eggs and to identify potential risk factors that may contribute to the presence of zoonotic pathogens in the flocks. One composite faecal sample was collected from each backyard (82 samples). Composite sampling here means taking one or more grab samples from a backyard to make up approximately 10 grams. Four per cent of samples, that is 4% backyards tested, were positive for Salmonella spp., 10% were positive for Campylobacter spp. and none were positive for Shigella spp. A higher infection rate was seen in multi‐aged flocks (24%) compared with the single‐aged flocks (3%). The survey found that many participants were engaging in risky food safety behaviours with 46% of participants responding that they washed their eggs with running water or still water instead of wiping the dirt off with a damp cloth to clean the eggs and 19% stored their eggs at room temperature. This study demonstrated that backyard poultry may pose a potential risk for salmonellosis and campylobacteriosis. Additionally, Australian public health and food safety regulations should be modified and effectively implemented to address the risks associated with backyard poultry husbandry. [ABSTRACT FROM AUTHOR]