Aberrations of the long arm of chromosome 13 are common in prostate cancer and were initially attributed to alterations of the RB1 gene in band q14 of the chromosome. However, prostate tumors generally yield normal p110RB1 nuclear staining despite loss of heterozygosity (LOH) at the RB1 locus. Our previous analysis of chromosome arm 13q showed allelic loss in 41% of primary prostate tumors. To refine our knowledge of 13q, we extended our previous LOH study by using more polymorphic markers to analyze more prostate tumors. Sixty human prostate carcinomas were screened for allelic loss on 13q by using 13 13q-specific markers. LOH on the long arm of chromosome 13 was found in 39 (65%) of the 60 tumors. Furthermore, 33 of these 39 tumors had evidence of allelic loss involving a region of 13q14 containing RB1. Because immunohistochemical assessment of pRb expression is controversial in prostate tumors, we used a quantitative reverse transcription polymerase chain reaction (RT-PCR) method to determine whether RB1 is the target tumor suppressor gene in this region. RB1 mRNA steady-state levels were determined in 12 prostate tumors preselected on the basis of presumed deletion at the RB1 locus and four prostate tumors without LOH at the RB1 locus; five normal prostate specimens were used as controls. One of the 12 assessable prostate tumors with presumed LOH at RB1 showed a corresponding decreased in RB1 mRNA expression, whereas none of the four tumors without LOH at RB1 locus showed such a decrease. This study, based on another technical approach, confirms that RB1 is not the main target of the observed LOH at 13q14.3, and raises the possibility that another tumor suppressor gene in this region plays a key role in prostate cancer.