A novel tumor suppressor gene, PTEN, which encodes a dual-specificity protein phosphatase, has recently been identified on chromosome 10q23. We have previously shown that both alleles of this gene are inactivated in three of four prostate cancer cell lines tested. To evaluate the role of inactivation of this gene in primary stage B prostate cancers, 60 cases were analyzed using Southern blotting with PTEN probes and microsatellites on 10q23. Eight of 60 cases had homozygous deletions by Southern blotting. In three of these cases, homozygous deletion was confirmed by apparent retention of heterozygosity at PTEN with loss of heterozygosity at telomeric and centromeric loci. In the remaining five cases, microsatellite analysis was consistent with homozygous deletion. Loss of heterozygosity at PTEN was found in only two cases both by microsatellite analysis and quantitative Southern blotting. No small mutations within PTEN exons were found in any tumors exhibiting alterations on 10q23. Thus, inactivation of the PTEN gene by homozygous deletion occurs in approximately 10-15% of primary stage B prostate carcinomas.