Annexin II mRNA coding for a calcium binding protein was found to be absent in prostate cancer by subtractive hybridization and Northern analysis. In contrast to high expression in normal and benign hyperplastic glandular and basal epithelium, Annexin II heavy (p36) and light (p11) chains in 31/31 prostate cancer specimens were lost immunohistochemically. In glands involved by prostate intraepithelial neoplasia, 65% lost both chains in glandular epithelial cells, whereas basal cells were all positively stained. Southern analysis of cancer DNA showed no noticeable deletion in p36 gene. LNCaP cells treated with 5-azacytidine re-expressed p36, suggesting methylation could be responsible for the silencing.