Although the significance of focally enhanced gastritis (FEG) as a marker of Crohn disease (CD) in adults has been contested, several studies suggest that it may be more specific of CD in pediatric patients. This study describes the detailed histologic features of FEG in pediatric inflammatory bowel disease (IBD) and clarifies its association with CD. A series of 119 consecutive newly diagnosed IBD patients (62 CD cases, 57 ulcerative colitis [UC] cases) with upper and lower gastrointestinal biopsies were evaluated. The histology of the gastric biopsies was reviewed blinded to final diagnoses and compared with age-matched healthy controls (n=66). FEG was present in 43% of IBD patients (CD 55% vs. UC 30%, P=0.0092) and in 5% of controls. Among CD patients, FEG was more common in younger patients (73% in children aged 10 y and below, 43% in children above 10 y of age, P=0.0358), with the peak in the 5- to 10-year age group (80%). The total number of glands involved in each FEG focus was higher in UC (6.4±5.1 glands) than in CD (4.0±3.0 glands, P=0.0409). Amongst the CD cohort, patients with FEG were more likely than those without FEG to have active ileitis (79% vs. 40%, P=0.0128) and granulomas elsewhere in the gastrointestinal tract (82% vs. 43%, P=0.0016). There was no correlation between FEG and other gastrointestinal findings of UC. We demonstrate that differences in FEG seen in pediatric CD and UC relate to not only their frequencies but also the morphology and relationship with other gastrointestinal lesions. Further, FEG is associated with disease activity and the presence of granulomas in pediatric CD.