OBJECTIVE To investigate the relationship between genomic heterogeneity and tumour grade, stage and DNA content in 30 transitional cell carcinomas (TCCs) of the urinary bladder. MATERIALS AND METHODS Tissue specimens from 30 patients (25 men and five women) with newly diagnosed TCC of the urinary bladder were examined for genomic heterogeneity using fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes; the copy number of pericentromeric sequences on chromosomes 7, 9 and 17 was detected within interphase nuclei in contact preparations from the tumour specimens. RESULTS The aneusomy of chromosomes 7, 9 and 17 was significantly higher in aneuploid than in diploid tumours (P < 0.001). Tumour grade and stage were strongly associated with aneusomy for chromosome 17 (P < 0.01, P < 0.001, respectively). The aneusomy of chromosomes 7 and 9 were significantly correlated with increasing tumour stage (P < 0.001), but not with tumour grade. CONCLUSION These results suggest that the measurement of aneusomy using FISH, especially for chromosome 17, in bladder cancer may offer a new objective and quantitative assay of the biological potential of individual tumours.