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We aimed to determine the prevalence of celiac disease (CD) in children with iron deficiency anemia (IDA) and compare the hematological variables of these children with those with IDA, but not with CD. A total of 250 patients aged 1 to 16 years with IDA were included. Upper gastrointestinal system endoscopy was recommended to the patients who were serologically positive for CD. According to the endoscopic biopsy results of 12 patients who have positive screening tests (57.1%), Marsh grade II histopathologic findings were detected in 1 (4.8%) and Marsh grade III histopathologic findings were detected in 11 (52%). The hemoglobin, hematocrit, iron, and ferritin levels were significantly lower in patients with CD with IDA, compared with those with IDA, but not with CD. According to Marsh classification, the percentage of Marsh grade IIIc was found to be higher than the other Marsh grades. As the Marsh grading increased, hemoglobin, hematocrit, serum iron, and ferritin levels decreased and tissue transglutaminase Ig A levels increased. Our results show that CD should be kept in mind as the underlying etiologic factor in patients with IDA.