Aims. Childhood radiation is a risk factor for thyroid cancer, which became well-known after the Chornobyl nuclear plant accident, where childhood thyroid cancer cases significantly increased afterward. Although these human cases have been extensively studied, the mechanisms of thyroid cancer susceptibility to radiation exposure at young ages have not yet been understood. Our previous investigations demonstrated that neonatal exposure to X-rays induced long-term mRNA expression changes in the thyroid cancer-related marker genes in rats. Then, we searched for the genes whose expressions were altered by neonatal radiation exposure in the rat model. Methods. Male Wistar rats at 1 and 8 weeks old were subjected to cervical X-irradiation (0-12 Gy). After 8 weeks, total RNAs were extracted from the thyroid and applied to RNA-seq analysis to identify the genes that neonatal irradiation alters the mRNA expressions. The expression changes were further examined in the thyroid of rats exposed to various doses of X-rays and in the iodine-deficient diet (LID) induced thyroid tumors. Results. 1) A comparison of thyroid gene expressions between neonate and adult irradiation found 9 up-regulated and 5 down-regulated genes related explicitly to neonatal radiation exposure. 2) These identified gene expressions were also altered in the thyroid tumors. 3) Combined treatment of radiation and LID further enhanced these gene expressions. Conclusions. An RNA-seq analysis showed that a neonatal single cervical irradiation brought long-term gene expression changes in the thyroid. Interestingly, these genes were also up-regulated in the LID-induced thyroid tumors. These alterations of gene expressions by neonatal radiation may be involved in the increased risk of thyroid cancer development by childhood radiation.