Objective: To investigate the relationship between Hashimoto’s thyroiditis (HT) and risk of papillary thyroid cancer (PTC), and its association with the prognosis of PTC patients. Methods: The data of 2 478 patients undergoing thyroid surgery in the first affiliated hospital of China Medical University between 2004 and 2012 were retrospectively analyzed. Of them, 676 were PTC patients, and 1 802 were benign thyroid nodular disease (BTND) patients. The incidence of concomitant HT, parameters for thyroid function tests and other possible influential factors of the two groups of patients were compared and analyzed. Results: Compared with BTND group, in PTC group, the rate of concomitant HT, level of thyroid stimulating hormone (TSH), and positive rate of thyroglobulin antibodies (TGAb) and thyroid peroxidase antibody (TPOAb) were significantly increased, but the free triiodothyronine (FT3) level was significantly increased (all P<0.05), while the sex ratio and free thyroxine (FT4) level showed no statistical difference (both P>0.05). After exclusion of the HT patients, both TGAb and TPOAb positive rates in PTC group were still higher than those in BTND group (both P<0.05), and in addition, the PTC ratio was elevated with the increase of TSH level in either the entire group of patients or HT patients only. In comparison between the BTND patients with and without HT, the former showed significantly reduced male ratio, significantly increased TSH level and significantly decreased FT3 and FT4 levels (all P<0.05). In comparison between the PTC patients with and without HT, the former showed significantly decreased male ratio and average age, and significantly increased TSH level, but reduced tumor size and TNM stage (all P<0.05). Multivariate analysis identified that concomitant HT, high TSH level, male sex and positive TGAb were independent risk factors for PTC (all P<0.05). Conclusion: HT is associated with an increased risk of PTC, which is probably associated with the increased TSH level induced by the hypothyroid status in HT. However, as an autoimmune disease, it may also be associated with a better prognosis of PTC patients.