ObjectiveTo investigate the relationship between prognosis of patients with primary clear cell renal cell carcinoma (ccRCC) after radical nephrectomy and expression of tumor metastasis-associated gene CD99 and to analyze the prognostic factors of ccRCC patients. MethodsSemi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) was used to examine the expression of CD99 in primary ccRCC tissues and their corresponding adjacent tissues. The prognosis and risk factors of survival time of patients were studied by follow-up investigation, and the main risk factors were screened by Cox hazard regression model. ResultsCompared with the adjacent renal tissues, 73.5% ccRCC tissues had up-regulated CD99 expression, with significant difference found between the two groups( P=0.000). Cox hazard regression model showed that high CD99 expression in ccRCC tissues was not a survival risk factor of ccRCC patients after radical nephrectomy (HR=0.14, 95%CI\[0.01,2.15\]); and age (HR= 1.18, 95%CI\[1.01,1.38\]), TNM stages (HR=51.91, 95%CI\[4.31,625.87\]), diabetes (HR=59.94, 95%CI\[2.21,1 627\]) and hypertension (HR=47.72, 95%CI\[1.37,1 670\]) were the major risk factors for the survival of patients after radical nephrectomy. The 1-year and 2-year survival rates of ccRCC patients in TNM stage Ⅰ were significantly higher than those in TNM stage Ⅱ-Ⅳ, respectively (100.0% vs 60.0%, P=0.004; 93.8% vs 8.3%,P=0.000). ConclusionThe expression of tumor metastasis-related gene CD99 may not be associated with the prognoses of ccRCC patients. Age, TNM stage, diabetes and hypertension are the major risk factors of prognosis after resection of ccRCC.