Aims: This study aimed to analyze the etiology of H.pylori-negative and/or gastrotoxic drug-negative peptic ulcers (HNGN-PU) in children and to investigate the difference of clinical features, endoscopic and laboratory findings of HNGN-PU according to the etiology including eosinophilic gastroenteritis (EoGE), systemic disease, and idiopathic peptic ulcers. Method: We retrospectively recruited 255 children with peptic ulcers (157 boys and 99 girls, aged 1 day – 18 years) between July 2003 and April 2017. We categorized the subjects into the 5 groups according to etiology; 1) H. pylori ulcers (n = 51); 2) gastrotoxic drugs ulcers (n = 18); 3) idiopathic peptic ulcers (n = 144); 4) systemic disease ulcers (n = 23); 5) EoGE ulcers (n = 19). Anastomosis site ulcer after gastrojejunostomy was excluded from the study. We reviewed and analyzed demographic data, clinical features, allergy history, endoscopic findings, and laboratory tests in all subjects included. Results: Age at diagnosis (p 0.001), ulcer recurrence (p = 0.016), atopic dermatitis history (p = 0.002), white blood cell counts (p = 0.008), eosinophils in blood (p = 0.013), platelet (p 0.001), albumin (p = 0.027), iron (p 0.001), erythrocyte sedimentation rate (p 0.001), high-sensitivity C-reactive protein (p = 0.016), and fecal calprotectin (p = 0.025) differed significantly among the 5 groups. As for endoscopic findings, gastric ulcers (p = 0.005), duodenal ulcers (p 0.001), multiple ulcers (p = 0.023) and gastric mucosal nodularity (p 0.001) differed significantly among the groups. Compared with EoGE ulcers with the others, patients with EoGE ulcers were significantly older in age (p = 0.022) and revealed higher rate of ulcer recurrence (p = 0.018), atopic dermatitis history (p = 0.001), and blood and tissue eosinophilia (p = 0.001 & p 0.001). Conclusion: Our study revealed that the prevalence of EoGE ulcers in pediatric patients with HNGN-PU was 10.2 %, much higher than previously reported. In children with HNGN-PU, ulcer recurrence, blood eosinophilia, and history of atopic dermatitis might provide high levels of clinical suspicion for EoGE, requiring thorough investigation of tissue eosinophils counts on the basis of endoscopic biopsy.