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The aim of our study was to investigate children's exposure to the flame retardants polybrominated diphenyl ethers (PBDEs) by analysing faecal content, a non-invasive matrix, as well as responses to an exposure-assessment questionnaire. A convenience sample of 61 parents with children (aged >3 months to <2 years) completed an online pre-tested questionnaire and provided faecal samples for analysis by high resolution gas chromatography/mass spectrometry. BDE-209 was the dominant congener in faecal samples adjusted to 8.3 ng/g dry weight (dw), with >80% samples above the limit of detection (LOD). BDE-47 (0.23 ng/g dw) and BDE-153 (0.03 ng/g dw) were each detected above the LOD in approximately 60% of samples. Age was associated with BDE-47 (−7%/month) and BDE-153 (−12%/month) concentrations in faeces, but not BDE-209. Other variables associated with PBDE concentrations included features of the home (carpet, pets) and behaviour (hand-to-mouth, removing shoes, using a car sunshade, frequency of walks outdoors). However, given the small sample size of this study additional research is required to confirm these findings. In this study we demonstrated that faeces may be a viable alternative to monitor human exposure to PBDEs, but further validation studies are required.This study provides the first report of BDE-209 biomonitoring in Australian children.Faeces, a non-invasive matrix, were used to assess PBDE exposure in young children (<2 years) exposure.BDE-47 and BDE-153 but not BDE-209 concentrations were significantly negatively associated with child's age age.Faeces may be a viable alternative to serum for biomonitoring, but more validation studies are required.