Alteration in epigenetic regulation of gene expression is a frequent event in human cancer. CpG island hypermethylation and downregulation is observed for many genes involved in a diverse range of functions and pathways that become deregulated in cancer. Paradoxically, global hypomethylation is a hallmark of almost all human cancers. Methylation profiles can be used as molecular markers to distinguish subtypes of cancers and potentially as predictors of disease outcome and treatment response. The role of epigenetics in diagnosis and treatment is likely to increase as mechanisms leading to the transcriptional silencing of genes involved in human cancers are revealed. Drugs that inhibit methylation are used both as a research tool to assess reactivation of genes silenced in cancer by hypermethylation and in the treatment of some hematological malignancies. Multidimensional analysis, evaluating genetic and epigenetic alterations on a global and locus-specific scale in human cancer, is imperative to understand mechanisms driving changes in gene dosage, and as a means towards identifying pathways driving cancer initiation and progression.