Background: Iron deficiency anemia (IDA) is a major public health problem among children worldwide. Iron deficiency without anemia (IDWA) is at least twice as common as IDA. Some studies propose that oral iron fortification can modify the infant’s gut microbiome leading to intestinal inflammation. Objectives: To determine whether oral iron therapy can lead to intestinal inflammation in children with IDA or IDWA. Patients and methods: Fifty-six patients aged 6 months to 16 years (median age 7.6 years) with IDA or IDWA were randomly assigned to receive either iron (III)-hydroxide polymaltose complex (IPC) 5mg/kg once daily (maximum dose 100 mg) or sucrosomial iron (SI) 1.4 mg/kg once daily (maximum dose 29.4 mg). Safety and efficacy were studied after 30 and 90 days of treatment. In addition, fecal calprotectin as a marker of intestinal inflammation was measured simultaneously and compared to results obtained before therapy. Results: A significant increase in serum ferritin was noted in both groups as the median ferritin level at baseline was 6.7 μg/L in the IPC group and 6.6 μg/L in the SI group, increasing to 15.9 μg/L and 12.1μg/L respectively, after 90 days of treatment. However, there was no significant change in fecal calprotectin in either group. In addition, no differences in the trend over time were observed between the two groups regarding fecal calprotectin, serum ferritin, and hemoglobin. Conclusions: IPC and SI were equally effective in treating IDA and IDWA. At the recommended doses, oral iron therapy does not seem to induce intestinal inflammation.