Recent studies suggest a role for p53 in prostate cancer progression. Although p53 mutations in primary prostate cancer tissues are relatively infrequent, they occur at significant levels in metastatic disease. Here we describe a novel approach to the molecular analysis of p53 in paired specimens of primary and metastatic prostate cancer that results in quantitative estimates of the extent of clonal expansion. In 20 pairs with 1 or both specimens p53 immunopositive and in 6 pairs with both specimens immunonegative, the frequency of mutations was estimated by microdissection of the cancer from fixed and sectioned tissues, isolation of the DNA followed by PCR amplification of p53 genomic fragments, and cloning of the PCR products into plasmid vectors. At least 90 clones/tissue specimen were screened for mutations by single-strand conformational polymorphism analysis. DNA from abnormally migrating single-strand conformational polymorphism samples was sequenced to confirm mutations. Missense mutations in exon 5, 7, or 8 were detected in 9 of 20 immunopositive pairs and in 1 of 6 immunonegative pairs. A marked heterogeneity of mutations in primary prostate cancer was apparent. The frequency of p53 mutations was greater in the metastases than in the primary tumors. In three immunopositive pairs, the same p53 mutation was demonstrated at a low frequency in the primary tumor but was demonstrated at a greater frequency in the metastasis, indicating relatively limited clonal expansion of cells harboring specific p53 mutations in the primary tumor, yet significant clonal growth at metastatic sites as determined by this novel method.