Recent studies have shown that functional polymorphisms at the MDM2 SNP309 T/G and p53 Arg72Pro may be associated with cancer susceptibility. However, the role of these polymorphisms on the risk of transitional cell carcinoma of the bladder (TCCB) and clinical outcome remains unknown. SNP309 and p53 Arg72Pro polymorphisms were genotyped in 227 patients and 266 control subjects. The association between each polymorphism, TCCB risk and clinical outcome was evaluated by using a logistic regression model, a Kaplan-Meier curve with the log-rank test, or a Cox proportional hazard model. No significant associations between the polymorphisms and TCCB risk were found. On the MDM2 SNP309, the TT patients with superficial TCCB tended to have a longer recurrence-free survival than the TG or GG patients after transurethral resection (P=0.074). On the p53 Arg72Pro, the Pro/Pro patients with superficial TCCB had a significantly lower risk for recurrence than the Arg/Pro or Arg/Arg patients [Hazard ratio (HR), 0.364; 95% confidence interval (CI), 0.14-0.93]. In contrast, the Pro/Pro patients following radical cystectomy showed a significantly poorer survival and a higher risk of disease-specific death than the Arg/Pro + Arg/Arg patients (HR, 2.76; 95% CI, 1.11-6.84). MDM2 SNP309 and p53 Arg72Pro polymorphisms might influence the clinical outcome of TCCB in a distinctive way between superficial TCCB and invasive TCCB. The results may reflect marked differences in the genetic background between superficial and an invasive type of TCCB.