Autoimmune thyroid diseases (AITDs), including Graves' disease (GD) and Hashimoto's disease (HD), are thyroid-specific autoimmune diseases; however, predicting prognosis is difficult. Follicular helper T (Tfh) cells play a critical role in the differentiation of B cells and can be divided into three distinct subsets (Tfh1, Tfh2, and Tfh17), each with different abilities to regulate B cell responses. To elucidate the roles of circulating Tfh cells in the pathogenesis and prognosis of AITDs, we determined their proportions in the peripheral blood of patients with AITD and genotyped single-nucleotide variants (SNVs) in the CXCR5 gene. The proportion of circulating Tfh1 cells in Tfh cells was significantly higher in patients with GD and HD compared with control subjects. In contrast, the proportion of circulating Tfh2 cells was significantly lower in patients with GD and HD compared with control subjects. The G allele of CXCR5 SNV3 was significantly more frequent in patients with severe HD compared with those with mild HD. Overall, increased circulating Tfh1 cells and decreased circulating Tfh2 cells may play an important role in the pathogenesis of AITDs. The G allele of CXCR5 SNV3 may have a role in HD severity.