The cumulative incidence of hypothyroidism, in 131I-treated patients with hyperthyroidism caused by Graves' disease, has been gradually increasing each year. Meanwhile, the role of the genes that control radiation sensitivity (GCRS) involved in 131I therapy is yet to be defined. The main purpose of the present study is to find GCRS that could indicate hypothyroidism in Graves' disease patients treated with 131I. Thyroid tissue was collected from 59 patients who were diagnosed with Graves' disease. GCRS (including Bcl-2, NF-κB, Survivin, Ku-70, Tob1, EGFR, Egr-1, TP-53, BRCA-1, and ATM) mRNA levels were analyzed with qRT-PCR before radioiodine therapy. Patients were followed up and then grouped by end-point outcomes. The association of the variation of target genes with susceptibility to hypothyroidism was analyzed. Altogether 44 patients were enrolled, including 11 men and 33 women with an average age of 44.79 ± 12.94 years. Based on their clinical outcomes after at least 2-year follow-up, 59% (26/44) patients were evaluated as hypothyroid, while the remaining 41% (18/44) patients were non-hypothyroid, including 18% (8/44) with persistent hyperthyroidism. The hypothyroid group showed significantly lower Ku-70 mRNA expression levels than the non-hypothyroid group (p = 0.022), whereas no significance was detected regarding other target genes (p > 0.1). Multivariate analysis showed that Ku-70 was significantly correlated with hypothyroidism after 131I treatment (p = 0.033). The opposing changes in mRNA expression levels of Ku-70 in patients with hypothyroidism indicate its potential as a prognostic marker for hypothyroidism induced by 131I treatment.