A comparative study of primary prostatic tumors utilizing conventional metaphase analysis of prostate tumor cultures and fluorescence in situ hybridization (FISH) analysis of paraffin-embedded tissue sections revealed significant differences in type and extent of cytogenetic aberrations. Clonal trisomy 7 was identified in two tumors by metaphase analysis of prostate cultures, but not confirmed in either case by FISH analysis. True gain of chromosome 8 was revealed by FISH analysis in malignant epithelium of four tumors but not in adjacent normal or hyperplastic glands. Neither gain nor loss of this chromosome was observed by metaphase analysis in any of the tumors. Significant monosomy and nullisomy of chromosome 10 was identified in one case by FISH, but no cells with gain or loss of chromosome 10 were observed by metaphase analysis. Significant loss of the Y chromosome was revealed in one tumor by FISH, but no cells with -Y were identified by metaphase analysis. Clonal loss of the Y chromosome was identified in two other tumors by metaphase analysis. Paraffin FISH analysis of these tumors revealed overall monosomy in both, although in one tumor there was extensive nodular loss of the Y chromosome. Paraffin FISH analysis permits identification of cytogenetic aberrations in areas identified as carcinoma (CaP), prostatic intraepithelial neoplasia (PIN), and benign prostatic hyperplasia (BPH). This technique appears more informative in defining the true extent and nature of cytogenetic aberrations in prostate cancer than metaphase analysis of prostate tumor cultures.