The prognostic significance of DNA index (DI), S-phase fraction, and heterogeneity determined by flow cytometric DNA analysis was assessed in a prospective study of 249 newly diagnosed transitional cell carcinomas of the bladder. The median observation time was 4.8 years. A total of 456 subpopulations were detected. The S-phases could be estimated in 299 subpopulations. A DI > 1.25 or an S-phase above 9.7%were strongly correlated to invasiveness.One hundred and ten patients were treated with transurethral resection (TUR). Relapse-free survival could not be predicted by the DNA-derived parameters. Univariate analysis of survival showed prognostic significance of diploidy (0.98 < DI 5 1.02, P = 0.021, hypotetraploidy (1.50 < DI 5 1.96, P = 0.0021, and S-phase size (P = 0.008). Multivariate analysis pointed to the T-classification (RR = 1.64) and hypotetraploidy (RR = 1.57) as prognostic parameters for survival of TUR-treated patients.One hundred and thirty-nine patients received radiotherapy (RT). A significantly better response was found for tumors with a subpopulation with a hypertetraploid DNA content (DI > 2.04, P = 0.051, and a significantly worse response for subpopulations with a maximum S-phase > 24.5% ( P = 0.04). T-classification and histological grade had no predictive value. A logistic regression analysis indicated an estimated probability of response to RT of 77% for tumors with a DI > 2.04 and an S-phase < 24.5%, whereas tumors with a DI < 2.04 and an S-phase > 24.5% had only a 28% probability of response. The poor response to RT, predicted by an S-phase > 24.5%, translated into a poor survival, whereas the better treatment response found for patients with a DI > 2.04 did not result in a longer survival. Multivariate analysis pointed to S-phase (RR = 1.701, T-classification (RR = 1.601, and grade (RR = 0.65) as independent prognostic parameters for survival of RT-treated patients. o 1995 Wiley-Liss, Inc.Key terms: Detergent-trypsin preparation, propidium iodide, chicken and trout erythrocyte standardization, multivariate analysis of survival, treatment response Transitional cell carcinoma of the bladder is a disease entity encompassing a wide spectrum of tumors ranging from relatively benign non-invasive neoplasms with a low capacity for progression to rapidly disseminating cancers with a high mortality rate. The best prognostic parameters in general use today are the T-classification and histological grade (9,19,22). These parameters are influenced by the subjectivity of the urologist and the pathologist ( 20) and therefore not completely reproducible. Furthermore considerable variation in the clinical course may be found for tumors of identical class and grade. There is thus a need for additional and preferentially objective measurements with prognostic significance in bladder cancer.The prognostic value of tumor DNA content has been recognised for a number of years (2). Flow cytometric DNA analysis yields information on stem-line DNA abnormality, heterogeneity, and S-phase size. These variables