Background: The objective of this study is to identify intact and deficient cognitive processes in children with attention deficit hyperactivity disorder (ADHD) and children with high functioning autism (HFA). Method: Three rigorously diagnosed groups of children aged between 6 and 12 years (54 ADHD, 41 HFA, and 41 normal controls) were tested on a wide range of tasks related to five major domains of executive functioning (EF): inhibition, visual working memory, planning, cognitive flexibility, and verbal fluency. In addition, the role of comorbid oppositional defiant disorder (ODD) and comorbid conduct disorder (CD) in ADHD was investigated by directly comparing 20 children with ADHD and 34 children with comorbid ADHD + ODD/CD. Results: ADHD was associated with EF deficits in inhibiting a prepotent response and verbal fluency. Children with HFA demonstrated deficits in all EF domains, except interference control and working memory. The HFA group showed more difficulties than the ADHD group with planning and cognitive flexibility. The comorbid ADHD + ODD/CD group did not show a distinctive pattern of performance on the EF tests compared to the ADHD group. Conclusion: The present study indicates that children with HFA exhibit more generalised and profound problems with EF tasks compared to children with ADHD.