Psychopathological, genetic and neuropsychological findings indicate an association between autism and attention deficit/hyperactivity disorder (ADHD). The goal of this study was to assess possible differences in facial affect recognition in children with autism (with and without comorbid ADHD), with ADHD and healthy controls. Children aged 6-18 years old with DSM-IV-diagnosis ADHD (n=30) or autism (n=40) were included consecutively in the study. Facial affect recognition was assessed with a computer-based program used for teaching emotion processing called the Frankfurt Test and Training of Social Affect (FEFA) using faces and eye-pairs as target material. Additionally three attention-tasks (Sustained attention, Inhibition, Set-Shifting) were administered. Approximately 52% of the autistic children met the criteria for the comorbid diagnosis of ADHD. A MANOVA with post-hoc Scheffé tests revealed a significant difference in the recognition of faces and eye pairs between the group ADHD and controls (P=0.009). Children with autism and ADHD also differed significantly from healthy participants in the recognition of eye-pairs (P=0.009). Neither correlations with PDD nor with ADHD symptom scores were able to explain these results. Sustained attention and inhibition deficits had a significant influence on emotion recognition in children with ADHD. Our findings imply that the ability of facial affect recognition is reduced in children suffering from ADHD symptoms, both in autistic and pure ADHD children. ADHD symptoms need to be taken into account in future studies assessing emotion recognition in autistic children and adolescents.