Objectives: The clinical significance of Helicobacter pylori-negative chronic gastritis (HPNCG) in children is unclear. We examined this issue in patients who had undergone esophagogastroduodenoscopy with systematic gastric sampling. Methods: Data of 1178 consecutive children who underwent diagnostic esophagogastroduodenoscopy were collected. Baseline characteristics and long-term outcomes were compared between children with active and inactive HPNCG and those with normal gastric histology. Follow-up data were available for up to 13 years. Results: Altogether 24 (2.0%) children had active and 235 (19.9%) inactive HPNCG, 27 (2.3%) were Hpylori-positive, 46 (3.9%) had other gastric pathology, and 846 (71.8%) normal histology. Diarrhea (31.3% vs 25.1%, P ¼ 0.033), poor growth (23.6% vs 14.7%, P < 0.001), bloody stools (13.9% vs 7.2%, P < 0.001), anemia (46.5% vs 23.4%, P < 0.001), hypersedimentation (39.7% vs 21.4%, P < 0.001), hypoalbuminemia (40.4% vs 16.2%, P < 0.001), and elevated fecal calprotectin (62.4% vs 31.5%, P < 0.001) were more common and heartburn (13.9% vs 22.9%, P ¼ 0.002) less common in the HPNCG group than in the controls. Both active (OR 3.64,95% CI 1.35-9.82) andinactive (2.98, 2.18-4.08) HPNCG predicted a diagnosis in the initial investigations. Crohn disease (41.7%) was the most common diagnosis in active HPNCG and celiac disease (37.4%) in inactive HPNCG. During follow-up, 7 (9.9%) of the 71 initially nondiagnosed HPNCG children received a diagnosis. Conclusions: HPNCG is a frequent finding in children undergoing EGD, the active form being associated especially with Crohn disease and the inactive with celiac disease. The long-term prognosis of patients with HPNCG who do not receive an initial diagnosis is good.