A family-based, cognitive behavioural treatment for anxiety in 47 children with comorbid anxiety disorders and High Functioning Autism Spectrum Disorder (HFA) was evaluated. Treatment involved 12 weekly group sessions and was compared with a waiting list condition. Changes between pre- and post-treatment were examined using clinical interviews as well as child-, parent- and teacher-report measures. Following treatment, 71.4% of the treated participants no longer fulfilled diagnostic criteria for an anxiety disorder. Comparisons between the two conditions indicated significant reductions in anxiety symptoms as measured by self-report, parent report and teacher report. Discussion focuses on the implications for the use of cognitive behaviour therapy with HFA children, for theory of mind research and for further research on the treatment components.