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Whole-body counter measurements of residents of Fukushima Prefecture have been extensively performed after the Fukushima Dai-ichi Nuclear Power Plant accident in March 2011. These measurements have demonstrated that the levels of internal contamination with radioactive cesium (134Cs and 137Cs) in the residents are very low. This article provides an overview of and lessons learned from these whole-body counter measurements with emphasis on the technical problems encountered, and it discusses the effective use of whole-body counters for assessing the internal thyroid doses of individuals when direct measurements of 131I in the thyroid are difficult or impossible to implement for the total affected population in a short time after a nuclear reactor accident. The application of this dose reconstruction method requires determining the intake ratio of 131I to cesium isotopes at appropriate times and considers the short biological half-lives of cesium isotopes, in particular for children.