Purpose <p>Autistic children have been shown to have poorer bone health than their non-autistic peers, but previous evidence on this topic has been based on small clinical samples and is limited by how bone health has been measured. The association between autism and bone health may also reflect confounding by correlated genetic or environmental factors, but prior studies have not addressed this issue.</p> Methods <p> We address these issues using data from a population-representative cohort of Australian children with bone health measured by peripheral quantitative computed tomography (pQCT) for both children and parents. Data for 1,274 children (66 autistic, 1,208 non-autistic) aged 11–12 years (50% male) were drawn from the Child Health CheckPoint within the Longitudinal Study of Australian Children. pQCT measures at the tibial diaphysis (ankle) and metaphysis (shin) were recorded using an identical protocol for children and one attending parent. Child autism was parent reported. Regression analyses were used to compare differences between autistic and non-autistic children, and between parents of autistic children and parents of non-autistic children.</p> Results <p> Our findings indicate poorer bone health as assessed by tibial pQCT among autistic children compared to non-autistic children at both the metaphysis and diaphysis. No differences in pQCT measures were found between parents of autistic and non-autistic children, suggesting no evidence of confounding by shared genetic or environmental factors.</p> Conclusion <p> These findings reinforce the need to support improved bone development among autistic children and suggest that differences in bone health are likely driven by behavioural factors that are potentially amenable to intervention.</p>