Marker chromosomes contain potentially valuable information about breakpoints in cancer. However, routine banding procedures, by themselves, provide only limited information about the identity of marker chromosomes. In this study, the use of fluorescence in situ hybridization (FISH) with chromosome-specific centromeric probes and whole-chromosome-specific DNA libraries greatly enhanced the identification of 10 marker chromosomes in the primary prostatic cancer cell line PPC-1. Centromeric probes for chromosomes 1, 2, 3, 4, 10, 12, and 17 and whole-chromosome paint libraries for chromosomes 1, 2, 3, 4, 8, and 12, in conjunction with analysis of G-banded metaphases, allowed the major portion(s) of these 10 PPC-1 marker chromosomes to be defined. The results increase the number of identifiable chromosomal breakpoints in this cell line from 9 to 28 sites.