Young people with autism spectrum disorder (ASD) have a high prevalence (~40 %) of anxiety disorders compared to their non-ASD peers. It is unclear whether cognitive and biological processes associated with anxiety in ASD are analogous to anxiety in typically developing (TD) populations. In this study 55 boys with ASD (34 with a co-occurring anxiety disorder, 21 without) and 28 male controls, aged 10-16 years and with a full-scale IQ ≥ 70, completed a series of clinical, cognitive (attention bias/interpretation bias) and biological measures (salivary cortisol/HR response to social stress) associated with anxiety in TD populations. Structural equation modelling was used to reveal that that both attentional biases and physiological responsiveness were significant, but unrelated, predictors of anxiety in ASD.