The purpose of this study is to compare the prevalence and types of diseases (International Classification of Mental and Behavioural Disorders, 10th Edition codes K20-K93) relating to the gastrointestinal tract in a clinical sample of 89 individuals diagnosed as children with atypical autism/pervasive developmental disorder not otherwise specified with 258 controls from the general population. All participants were screened through the nationwide Danish National Hospital Register. The average observation time was 32.9 years, and mean age at the end of the observation period was 48.5 years. Among the 89 cases with atypical autism, a total of 22 (24.7%) were registered with at least one diagnosis of any disease of the gastrointestinal tract, against 47 of 258 (18.2%) in the comparison group (p = 0.22; odds ratio = 1.5; 95% confidence interval = 0.8-2.6). Without reaching statistical significance, the rate of diseases of the gastrointestinal tract was particularly high (odds ratio = 1.2) in those with intelligence quotient less than 70. Overall, people with atypical autism had about the same frequency of gastric, intestinal and hepatic diseases as had controls. (Contains 2 tables.)