Mycobacterium paratuberculosis, the causative agent of Johne's disease (a chronic enteritis in ruminants), has been suspected to be involved in Crohn's disease. In this study, polymerase chain reaction was used to detect the presence of IS900 DNA sequences specific to M. paratuberculosis genomes in biopsies and surgical resections from 53 children with various gastrointestinal diseases and disorders. IS900 sequences were found in 13 of 18 samples from patients with Crohn's disease (72%; P < .01 vs. samples from patients without Crohn's disease), in 1 of 5 with ulcerative colitis, in 2 of 6 with severe unclassified colitis, and in 7 of 24 with other gastrointestinal illnesses. These results appear to support the hypothesis that M. paratuberculosis is involved in the pathogenesis of Crohn's disease.