Although autoimmune atrophic gastritis is classically a disease of elderly adults, recent studies have described the disease in younger adults, particularly in those with other autoimmune diseases and iron-deficiency anemia. Atrophic gastritis in pediatrics is a rare and possibly underdiagnosed entity that has been primarily reported as single-case reports. This retrospective study of atrophic gastritis not associated with Helicobacter pylori infection was performed to further expand the knowledge of clinical presentation, pathologic findings, and natural history of this disease in the pediatric population. Twelve patients with a histologic diagnosis of atrophic gastritis were identified, with an age range of 8 months to 18 years. Seven had other autoimmune diseases and/or immunodeficiency. Atrophy was confined to the oxyntic mucosa in 10 patients, with intramucosal inflammation in a diffuse or basal-predominant pattern. Active inflammation was present in 7 patients. Pseudopyloric, intestinal, or squamous/mucinous metaplasia was seen at initial biopsy or on follow-up in 8 patients, and enterochromaffin-like cell hyperplasia was seen in 5. One patient developed an adenocarcinoma during the follow-up period of 10 years. Two false-negative diagnoses were retrospectively identified. In the majority of cases, the possibility of atrophic gastritis was not raised by the submitting physician, and the endoscopic findings were not specific. Therefore, accurate diagnosis requires a high degree of suspicion on the part of the pathologist, and the diagnosis should be considered particularly in patients with a clinical history of other autoimmune diseases or iron-deficiency anemia.