The most frequent genetic aberration found in transitional cell carcinoma (TCC) of the bladder involves chromosome 9. Loss of heterozygosity (LOH) analyses show deletions of both chromosome 9p and 9q, while in situ hybridization studies suggest a significant percentage of tumours with monosomy 9. To investigate the types of chromosome 9 losses that occur in bladder cancer, we have studied 40 tumours with different techniques such as in situ hybridization (ISH), flow cytometry and LOH analysis. LOH for one or more markers was found in 43% of the tumours. This percentage does not differ from previous reports. With ISH, complete monosomy for chromosome 9 was observed in only 1 of the 40 tumours. Four other tumours had monosomic subpopulations, representing 23-40% of the cells. In 18 cases, an underrepresentation of the chromosome 9 centromere relative to chromosome 6 or to the ploidy of the tumour was observed, including the cases with monosomy. In 5 of these 18 cases, the relative loss could not be confirmed by LOH. In addition, when LOH and a relative underrepresentation were observed in the same tumour, the extent of LOH as measured by the intensity of allele loss, was often not related to the extent of underrepresentation. We therefore conclude that complete monosomy of chromosome 9 is rare in TCCs of the bladder and that a relative loss of centromere signal may not be related to a loss compatible with inactivation of a tumour suppressor gene. LOH was found in TCCs of all stages and grades. Our results suggest that loss of tumour suppressor genes on chromosome 9 is an early event in the pathogenesis of bladder cancer.