In the development of prostate cancer there is an important transition from androgen-dependent growth (which can be treated) to androgen-independent growth (which is beyond medical control). This transition is probably accompanied by genetic changes, resulting in the activation of oncogenes or the inactivation of tumor suppressor genes. In the present manuscript, the isolation of genes that may be involved in advanced, androgen-independent prostate cancer growth is described. Using differential display PCR, 13 cDNAs were isolated representing genes that are differentially expressed between the androgen-dependent prostate carcinoma cell line LN-CaP and the androgen-independent prostate carcinoma cell lines PC-3 and DU 145. These clones were divided into four groups: androgen-responsive genes (TL5, TL25, TL32, and TL35); genes with a marked decreased expression in one of the prostate cancer cell lines (TL27); genes with a marked, increased expression in one or more of the prostate cancer cell lines (TL4, TL16, TL21, and TL22); and genes with minor (but repeatable) changes in expression between prostate cancer cell lines (TL7, TL15, TL18, and TL33). The 13 genes were analyzed for their sequence information, tissue specificity, and androgen responsiveness in order to identify genes of interest. In summary, differential display PCR appears to provide an attractive alternative to existing molecular techniques to screen for differentially expressed genes in prostate cancer cells.