Intestinal diseases are regarded as a common cause of anemia, but the diagnostic outcomes of children with anemia undergoing endoscopic investigations are unclear. We investigated this issue in a large cohort of children. Indications for and findings of consecutive gastrointestinal (GI) endoscopies were collected. Clinical presentation and diagnostic outcomes were compared between anemic and nonanemic patients and between anemic patients with and without a diagnosis. Diagnoses received during follow-up were collected. Of 2395 consecutive endoscopies, 251 children with and 613 children without anemia had undergone either diagnostic esophagogastroduodenoscopy (EGD) (51.4% and 51.4%, respectively), colonoscopy (4.0% and 11.4%), or both (45.8% and 37.8%). Children with anemia more often received diagnoses (72.9% vs 39.3%; odds ratio [OR], 4.18; 95% confidence interval [CI], 3.03-5.77), particularly of celiac disease (26.3% vs 15.5%, P< .001) and of inflammatory bowel disease (31.1% vs 9.1%, P<.001), than did nonanemic children. The diagnosis in anemic patients was predicted by age 5 to 12 years (OR, 3.52; 95% CI, 1.27-9.75), presence of diarrhea (OR, 2.04; 95% CI, 1.07-3.90), melena/hematochezia (OR, 2.40; 95% CI, 1.17-4.92), poor growth (OR, 3.94; 95% CI, 1.70-9.15), positive celiac serology (OR, 11.81; 95% CI, 3.47-40.12), high calprotectin (OR, 12.86; 95% CI, 4.00-41.32), hypersedimentation (OR, 2.65; 95% CI, 1.29-5.44), and hypoalbuminemia (OR, 5.05; 95% CI, 1.56-16.34). Thirty children with anemia (12.0%) had no GI symptoms, and 22 of them (73.3%) were given diagnoses at the time of the endoscopies. All 22 had additional laboratory abnormalities, whereas these were present in only 2 of 8 undiagnosed children. None of them was diagnosed later in the follow-up of up to 11 years, in contrast to 4 (6.7%) of all anemic and 33 (8.9%) of all nonanemic patients. Anemia increased the probability of being given a diagnosis, emphasizing its importance as an alarm symptom. However, endoscopies in anemic patients without additional symptoms or laboratory abnormalities seldom improved the diagnostic yield.