The aim of the study was to evaluate the clinicopathological and prognostic significance of morphological subtyping of papillary renal cell carcinoma (PRCC). The patients treated for renal cell carcinoma in our department from January 1985 to March 2006 were evaluated retrospectively. Thirty-two of the 591 patients (5.4%) were diagnosed with PRCC. To determine the prognostic factors, we re-evaluated the pathological stage according to the 2002 TNM classification of malignant tumors, and the tumor type of renal cell carcinoma according to the 2004 World Health Organization histological classification. Survival was analysed using the Kaplan-Meier method and the log-rank test. The age at diagnosis ranged from 33 to 81 years (median: 63 years old) and the follow-up time after the surgical treatment ranged from 4 to 191 months (median: 54 months). The cancer-specific 5-year survival rate of the 32 PRCC patients was 74%. Pathologically, 17 patients (53%) and 15 patients (47%) were diagnosed with type 1 and type 2 PRCC, respectively. The type 2 PRCC patients had a significantly higher tumor grade (P < 0.001), a more advanced stage (P < 0.001), more frequent vascular invasion (P < 0.001), and a higher sarcomatoid component (P = 0.038) compared to the type 1 PRCC patients. The type 1 patients had a better cancer-specific 5-year survival rate than the type 2 patients (94% vs 50%) (P = 0.008). The morphological subtyping of PRCC is significantly associated with clinicopathological features and the prognosis. Our results provide evidence of the clinical utility of dividing PRCC into two subtypes.