Bloom's syndrome (BS) is an autosomal recessive disorder with a high cancer incidence. BS cells exhibit increased chromosomal instability and sister-chromatid exchange. The rate of spontaneous mutation at the locus encoding hypoxanthine phosphoribosyltransferase (HPRT) in a lymphoblastoid cell line derived from a BS patient, GM3403, was 1.39 x 10(-6) mutations/cell/generation, whereas that in TK6, a lymphoblastoid cell line derived from an individual who is not suffering from BS, was 1.75 x 10(-8) mutations/cell/generation. Molecular analysis of the HPRT gene in mutant clones by multiplex polymerase chain reaction revealed that 83.3% of the spontaneous mutants from GM3403 cells contained deletions at the HPRT locus, whereas 30.8% of mutants from TK6 cells had deletions. Approximately half of the BS mutants had lost the entire gene. Some mutant clones of GM3403 had also lost markers near the HPRT locus, although no mutant clones from TK6 cells had lost these markers. These results indicate that the mutator phenotype of BS cells is mainly due to an increase in large DNA alterations, reflecting the remarkable genomic instability that could be responsible for cancer proneness in this disease.