There is considerable controversy as to whether there is an association between bowel disorders and autism. Using a bowel symptom questionnaire we compared 51 children with autism spectrum disorder with control groups of 35 children from special school and 112 from mainstream school. There was a significant difference in the reporting of certain bowel symptoms (constipation, diarrhoea, flatulence) and food faddiness between the autism group and the mainstream school control group. There was no significant difference between the autism group and children in the special schools except for faddiness, which is an autism specific symptom and not a bowel symptom. This study confirms previously reported findings of an increase in bowel symptoms in children with autism. It would appear, however, that this is not specifically associated with autism as bowel symptoms were reported in similar frequency to a comparison group of children with other developmental and neurological disorders.