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Background: The use of computed tomography (CT) device has increased in the past few decades in Japan. Dose optimization is strongly required in pediatric CT examinations, since there is concern that an unreasonably excessive medical radiation exposure might increase the risk of brain cancer and leukemia. To accelerate the process of dose optimization, continual assessment of the dose levels in actual hospitals and medical facilities is necessary. This study presents organ dose estimation using pediatric cerebral CT scans in the Kyushu region, Japan in 2012 and the web-based calculator, WAZA-ARI (https://waza-ari.nirs.qst.go.jp). Materials and Methods: We collected actual patient information and CT scan parameters from hospitals and medical facilities with more than 200 beds that perform pediatric CT in the Kyushu region, Japan through a questionnaire survey. To estimate the actual organ dose (brain dose, bone marrow dose, thyroid dose, lens dose), we divided the pediatric population into five age groups (0, 1, 5, 10, 15) based on body size, and inputted CT scan parameters into WAZA- ARI. Results and Discussion: Organ doses for each age group were obtained using WAZA-ARI. The brain dose, thyroid dose, and lens dose were the highest in the Age 0 group among the age groups, and the bone marrow and thyroid doses tended to decrease with increasing age groups. All organ doses showed differences among facilities, and this tendency was remarkable in the young group, especially in the Age 0 group. This study confirmed a difference of more than 10- fold in organ doses depending on the facility and CT scan parameters, even when the same CT device was used in the same age group. Conclusion: This study indicated that organ doses varied widely by age group, and also suggested that CT scan parameters are not optimized for children in some hospitals and medical facilities.