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Objective To explore the clinicopathological features and relative prognostic risks of the three major variants of papillary thyroid carcinoma (PTC). Methods We retrospectively analyzed the clinicopathological characteristics and prognoses of patients with the three major PTC variants, conventional papillary thyroid carcinoma (CPTC), follicular-variant papillary carcinoma (FVPTC), and tall-cell papillary thyroid carcinoma (TCPTC), based on data from the Surveillance, Epidemiology, and End Results database from 2005 to 2009. Results A total of 29,555 patients were enrolled. In terms of their demographic and clinicopathological characteristics, TCPTC had the highest prevalence of older patients, men, patients with locally advanced stage (T stage and N stage), and mortality, while FVPTC had the lowest prevalence in relation to these factors. The three variants differed significantly in terms of 5-year overall survival and 5-year disease-specific survival. Cox regression analysis identified male sex, age ≥45 years, and higher American Joint Committee on Cancer and TNM stage as independent factors predicting a poor prognosis in relation to both overall and disease-specific survival. Conclusions CPTC, FVPTC, and TCPTC have different clinicopathological characteristics and prognoses, indicating the need for different treatment strategies for these three variants of PTC.