Using the polymerase chain reaction followed by single-strand conformation polymorphism (PCR-SSCP) analysis and direct nucleotide sequence determination, the p53 gene was analyzed in six fresh leukemia samples from which cell lines with p53 mutations were established. Mutations of the p53 gene which were identical to those in the cell lines were observed in three of the fresh samples. In the other three samples, p53 gene mutations were not detected by the conventional PCR-SSCP method. However, when analyzed using allele-specific gene amplification, less than 10% of the leukemic cell population of the three samples, which were below the detection threshold of PCR-SSCP, were shown to have p53 gene mutations. Two samples taken at the initial presentation of two patients, whose relapse samples were shown to contain p53 mutant clones, were also available for analysis. A small population of clonal cells, comprising less than 1% of the population, was shown to have p53 gene mutations in both of these initial samples. These observations provide a potential biologic basis for the frequent findings of p53 mutations in leukemia cell lines and also suggest a potential role for p53 mutations in the clonal overgrowth of cells responsible for relapse of the disease.