Six sites of the Pediatric Inflammatory Bowel Disease Consortium (plus 2 additional sites) will participate in this study. The participating sites will be that of the Principal Investigator (PI), Emory University School of Medicine, Atlanta, GA (Benjamin D. Gold, MD); Texas Children's Hospital / Baylor College of Medicine (George Ferry, MD and Tony Olive, MD); Children's Hospital of Philadelphia, Philadelphia, PA (Bob Baldassano, MD); University of Chicago Children's Hospital, Chicago, IL (Barbara Kirschner, MD); University of California, San Francisco (Mel Heyman, MD); Mass General Hospital / Harvard University (Harland Winter, MD); V.A. Stanford University School of Medicine, Stanford, CA (David Relman, MD); Children's Center For Digestive Healthcare, Atlanta, GA (Stanley Cohen, MD); and Centers for Disease Control and Prevention, Atlanta, GA (Drs. Jeannette Guarner, Siobhan O'Connor and Thomas Shinnick)

The duration of study is 2 yrs.

Objectives:

1. Improve the methods to collect biopsies from the colon and ileum, tissue storage techniques and best methods to detect specific infections in children with Crohn's disease;
2. Determine if there are specific infectious agents that are more common in children with Crohn's disease, and;
3. Determine if there are types of children with Crohn's disease (e.g., children living in Boston, African American children) who may be more at risk for getting the infections.

The study design involves children ages 6 months through 17 11/12 years of age who are undergoing a clinically-indicated colonoscopy. Subjects will be grouped into cases and controls.

• Any child ages 6 mos through 17 11/12 years of age, undergoing a clinically-indicated colonoscopy as determined by the treating physician, is eligible for enrollment. About 500 patients will be enrolled in this study.
• Cases will consist of those children within the defined age group, who are undergoing diagnostic colonoscopy and have the definitive diagnosis of Crohn's disease.
• Children who have the diagnosis of indeterminate colitis or ulcerative colitis for the purpose of this R03, will be excluded as cases and from initial analysis, but will have tissue specimens banked for subsequent evaluation for infectious agents.
• Controls will consists of children within the defined age group, undergoing clinically indicated colonoscopy and who are not diagnosed with Crohn's disease, ulcerative colitis or indeterminate colitis (e.g., juvenile polyps, irritable bowel syndrome or functional bowel disease).
• Stool specimen (5ml/1 tsp) will be collected to test for different types of bacteria
• A questionnaire will be administered to each research volunteer.
• Each subject's medical information (i.e. diagnosis, disease stage, and laboratory results) will be stored electronically in a separate access-based database. A unique identifier will be assigned to each patient entered into the study and will also be used for blinding of the specimens analyzed by the pathologist and by molecular assays for infectious agents.
• Colonoscopy will be performed by the treating pediatric gastroenterologist and biopsies obtained in the usual standard of care.
• Clinical biopsies from the rectum, left, right, transverse colon and cecum will be placed in formalin containing vials as per standard of care for the clinical pathologist and diagnostic evaluation.