The clinical significance of focal neutrophilic infiltrates in crypt epithelium in colorectal biopsies or focal active colitis has been studied in adult populations, but little is known about this entity in children. The incidence of Crohn's disease in adult patients presenting with focal active colitis has varied between 0% and 13% in previous studies, whereas the incidence of infectious-type colitis has been reported to be nearly 50%. We reviewed 31 cases of focal active colitis diagnosed in pediatric patients without a history of inflammatory bowel disease between 1989 and 2000. Pathologic variables studied included number and location of inflamed crypts and distribution and character of lamina propria inflammation. Clinical follow-up was obtained from patient charts. Two patients were lost to follow-up. Follow-up on the remaining 29 patients ranged from 4 months to 7 years with a mean of 4.2 years. Eight patients (27.6%) developed Crohn's disease. Nine patients (31%) appeared to have acute infectious-type colitis, one with C. difficile. Eight patients (27.6%) had focal active colitis, which did not correlate with their symptoms or ultimate clinical diagnosis. These were termed idiopathic focal active colitis. Two patients were found to have allergic colitis, one had ulcerative colitis, and one had Hirschsprung's disease. Pediatric patients with focal active colitis have a much higher incidence of Crohn's disease than adults with same entity. Hence, it is important to document the presence of focal active colitis in pediatric patients.