Alterations in DNA methylation, which are associated with DNA methyltransferase abnormalities and result in silencing of tumor-related genes and chromosomal instability, are involved even in precancerous changes in various organs. DNA methylation alterations also account for the histological heterogeneity and clinicopathological diversity of human cancers. Therefore, we have analyzed DNA methylation on a genome-wide scale in clinical tissue samples. Our approach using the bacterial artificial chromosome array-based methylated CpG island amplification method has revealed that DNA methylation alterations correlated with the future development of more malignant cancers are already accumulated at the precancerous stage in the kidney, liver and urinary tract. DNA methylation profiles at precancerous stages are basically inherited by the corresponding cancers developing in individual patients. Such DNA methylation alterations may confer vulnerability to further genetic and epigenetic alterations, generate more malignant cancers, and thus determine patient outcome. On the basis of bacterial artificial chromosome array-based methylated CpG island amplification data, indicators for carcinogenetic risk estimation have been established using liver tissue specimens from patients with hepatitis virus infection, chronic hepatitis and liver cirrhosis or histologically normal urothelia, and for prognostication using biopsy or surgically resected specimens from patients with renal cell carcinoma, hepatocellular carcinoma and urothelial carcinoma. Such genome-wide DNA methylation profiling has now firmly established the clinical relevance of translational epigenetics.