BACKGROUND: Hashimoto’s thyroiditis (HT) is thought to be associated with an increased risk of papillary thyroid cancer (PTC). To investigate the possible impact of HT on the prognosis of patients with PTC, we evaluated clinical factors associated with it, especially serum thyroid-stimulatinghormone (TSH) levels. Materials and methods: A retrospective analysis of 2478 patients who underwent thyroid surgery between 2004 and 2012 was performed, comparing general demographic characteristics such as gender and age, as well as serum TSH levels, thyroid autoantibodies and other factors that may influence PTC. Results: Compared with patients with benign nodular thyroid disease, patients with PTC had a higher rate of HT comorbidity (18.8% vs. 7.2%, P<0.001), higher serum TSH levels (2.02±1.76 mIU/L vs. 1.46±1.21 mIU/L, P<0.001), and a higher rate of TGAb, TPOAb positivity (40.0% vs. 20.4%, P<0.001; 24.8% vs. 12.5%, P<0.001). The above results still held after excluding all HT patients. Serum TSH levels were significantly higher in PTC patients with combined HT than in those without (2.54±2.06mIU/L vs 1.90±1.66mIU/L, P=0.001). PTC patients with combined HT had younger age, higher proportion of women, smaller tumor size, and lower grade TNM stage than those without combined, suggesting that PTC patients with HT may have a better prognosis. In a multifactorial analysis, combined HT, high TSH levels, males, and TGAb positivity were shown to be independent risk factors for PTC. Conclusions: Pathologically diagnosed HT is associated with an increased risk of PTC, mainly because the hypothyroid tendency of HT can cause elevated serum TSH levels. In contrast, autoimmunity, another independent factor increasing the risk of PTC, may improve its prognosis.