Iron deficiency anemia (IDA) can be caused by occult gastrointestinal (GI) blood loss; however, the endoscopic findings in children with anemia are unclear. The study aimed to determine the frequency and factors related to lesions in children with IDA undergoing endoscopy. We retrospectively analyzed the clinical and endoscopic findings of children with a laboratory-based diagnosis of IDA. Of 58 patients, 36 (62.1%) had upper GI tract lesions, with erosive gastritis being the most common lesion. Further, 26 patients underwent concomitant colonoscopy, and 12 (46.2%) had lower GI tract lesions. Overall, 44 (75.9%) patients had lesions in either the upper or lower GI tract. infection was detected in 13 patients (22.4%). Patients with lesions found by endoscopy had significantly lower hemoglobin level (8.9 10.0 g/dL,  = 0.047) and mean corpuscular volume (75.5 80.9 fL,  = 0.038). The proportion of patients with previous treatment for IDA was also higher in those with lesions on endoscopy. In multivariate analysis, age of ≥10 years (odds ratio [OR], 6.00; 95% confidence Interval [CI], 0.56-10.75) and positive fecal occult blood test (FOBT) findings (OR, 2.25; 95% CI, 0.14-4.52) were factors related to GI lesions. The presence of GI symptoms was not associated with GI lesions. A high proportion of GI lesions were found by endoscopy in children with IDA in this study. Endoscopy should be considered in children with IDA even without GI symptoms, especially in older children, and those with positive FOBT results.