Methylation of CpG dinucleotides is an epigenetic mechanism involved in the regulation of gene expression in mammals. The patterns of CpG methylation are specie and tissue specific. The biological machinery of this system comprises a variety of regulatory proteins including DNA methyltransferases, putative demethylases, methyl-CpG binding proteins, histones modifying enzymes and chromatin remodeling complexes. DNA methylation maintains gene silencing and participates in normal development, genomic imprinting and X chromosome inactivation. In contrast, alterations in DNA methylation participate in the induction of some human diseases, especially those involving developmental defects and tumorigenesis. This review summarizes the molecular aspects of DNA methylation and its implications in cancer and other human diseases in which this epigenetic mechanism has been involved. Our understanding of the epigenetic changes that occur in human diseases will be very important for future management. Changes in the patterns of methylation can be used as markers in cancer and their potentially reversible state creates a target for therapeutic strategies involving specific gene re-activation or re-silencing.