Specific chromosomal losses have been reported for various human tumors. We have now investigated ten cases of urothelial carcinoma and observed genomic alterations by a new method allowing detection of chromosomal losses directly in the tissue section. In 6 out of 8 male carcinomas, the Y-chromosome was lost either in single cells and isolated areas or in extended regions of the tumor sample. Presence of chromosome 1 served as an internal control. This new in situ method allows studies of chromosomal alterations in relation to their tumor topology and the observations constitute the first report on such localised tumor-specific genomic changes.