We compared clinical and pathological staging in a contemporary, consecutive series of patients treated with partial or radical nephrectomy for renal cell carcinoma and we determined the effect of clinical and pathological stage discrepancy on outcomes. We collected retrospective clinical, pathological and survival data on 264 consecutive patients with clinical T1-3 renal cell carcinoma who were treated with laparoscopic or open partial or radical nephrectomy at a single institution from 1994 to 2003. Pathological up staging occurred in 44 of 264 patients (17%) patients. Of 135 clinical T1 tumors 25 (18.5%) and 18 of 85 (21.2%) clinical T2 tumors were pathologically up staged. Patients with clinical T1 and T2 tumors were stratified into 2 groups, including those with the same clinical and pathological stage, and those with pathological up staging. Mean 5-year recurrence-free survival +/- SD for same stage vs pathologically up staged clinical T1 (84.3% +/- 4.4% vs 47.4% +/- 11.5%) and clinical T2 (80.0% +/- 6.8% vs 40.7% +/- 13.4%) tumors was significantly different (p < 0.0002). Five-year cancer specific survival for same stage vs pathologically up staged clinical T1 tumors was significantly different (98.5% +/- 1.5% vs 69.7% +/- 11.3%, p = 0.0005), while that for clinical T2 tumors approached clinical significance (90.9% +/- 5.0% vs 72.7% +/- 13.4%, p = 0.0501). Stage discrepancy is common in surgically treated patients diagnosed with renal masses and it has a significant impact on clinical outcome. Implications of such clinical and pathological stage discrepancy should be considered when counseling patients and determining therapeutic approaches.