We conducted a quantitative analysis of the extent of de novo methylation of four CpG islands in human urinary transitional cell carcinomas of different stages and grades to determine how frequently these CpG islands became methylated in transition cell carcinomas during progression. The CpG islands included exon 5 of PAX6, exon 2 of p16, the 5' end of the deleted in bladder cancer gene, and the 5' end of transmembrane protein containing epidermal growth factor and follistatin domains. These sequences were not methylated in normal urothelial tissues; however, 48 of the 54 tumors examined (89%) showed methylation levels in excess of 20% for at least one of the markers. The number of markers concurrently methylated in individual tumors increased with the stage of the tumor, with several of the more aggressive invasive cancers showing hypermethylation of all four markers compared with the less aggressive invasive cancers. However, considerable methylation defects were present in superficial, preinvasive, papillary tumors. These data demonstrate that 89% of bladder cancers have increased methylation of CpG islands relative to their normal counterparts and suggest the occurrence of a hypermethylator phenotype in which multiple independent CpG islands become concurrently methylated in individual tumors in a process associated with tumor progression.