I have read countless times, parental tales of woe about their autistic children's constipation. yeasty poos, diarrhoea, and all sorts of bowel problems. No doubt, many of these are real, but reporting is rather self selecting. Most parents whose autistic children have no gut issues don't make as much noise. Moreover, constipation etc is common in all children.
In the past week, 2 scientific studies have been published that cast doubt on the validity of the autism gut connection. These are ably discussed on LB/RB.
The first study compared the stool patterns of autistic children and non-autistic children and concluded,
"During the first 42 months of life, ASD children had a stool pattern that was very similar to that of other children, apart from a slight increase in stool frequency at 30 and 42 months. There were no symptoms to support the hypothesis that ASD children had enterocolitis."