Recent studies have identified several chromosomal regions that are altered in prostate cancer. However, the specific genes affected are, in most of the cases, not known. Cancer cell lines could provide a valuable resource for cloning of genes that are commonly affected in cancer. The first step in the identification of such genes is the detection of chromosomal aberrations. Here, we have used comparative genomic hybridization (CGH) to screen for genetic alterations in four prostate cancer cell lines, LNCaP, DU145, PC-3, and TSU-Pr1. The analysis showed that, except for the LNCaP, these cell lines contained many genetic changes (> or = 10 per cell line), suggesting that they resemble genetically more closely hormone-refractory or metastatic than primary prostate carcinomas. All the chromosomal regions that have been implicated in prostate cancer were altered in at least one of the cell lines. The most common genetic changes were gain at 11q and losses at 6q, 9p, and 13q, each present in at least three cell lines. Identification of genetic aberrations by CGH in these cell lines should facilitate the choice of individual cell lines for cloning of genes that are involved in the development and progression of prostate cancer.