In order to establish an organ and effective dose database for Iranian children undergoing computed tomography (CT) examinations, in the first step, two Iranian 11-year-old phantoms were constructed from image series obtained from CT and magnetic resonance imaging (MRI). Organ and effective doses for these phantoms were calculated for head, chest, abdomen–pelvis and chest–abdomen–pelvis (CAP) scans at tube voltages of 80, 100 and 120 kVp, and then they were compared with those of the University of Florida (UF) 11-year-old male phantom. Depth distributions of the organs and the mass of the surrounding tissues located in the beam path, which shield the internal organs, were determined for all phantoms. From the results, it was determined that the main organs of the UF phantom receive smaller doses than the two Iranian phantoms, except for the urinary bladder of the Iranian girl phantom. In addition, the relationship between the anatomical differences and the size of the dose delivered was also investigated and the discrepancies between the results were examined and justified.