In the present study, different stages of transitional cell carcinoma of the bladder were analyzed by fluorescent in situ hybridization, using probes specific for pericentromeric classical satellite. Seventy primary tumors were evaluated for chromosomes 1, 7, 9, 17, and ploidy by flow cytometry. The results were correlated, after a mean follow-up period, with ploidy, histopathological characteristics, recurrence, and progression. Firstly, our data demonstrated that the sensitivity of fluorescence in situ hybridization in detecting quantitative DNA aberrations exceeds that of flow cytometry. The frequency of chromosome 1 and 9 aberrations was not significantly different in diploid and aneuploid tumors of different stage and grade. In contrast, the chromosome 7 and 17 aneusomy showed greater differences between pT1 and pT2-3 tumors (P<0.032 and P<0.0006, respectively) than between stage pTa and pT1. An increasing number of aberrations was observed in all chromosomes examined from tumors of patients that afterwards underwent cystectomy and/or had recurrent tumors. This study indicates that fluorescence in situ hybridization could be used to detect genetic changes relevant to patient outcome. These genetic changes could identify patients at high risk of recurrence and possible progression.