Hypermethylation of tumor suppressor genes caused by aberrant activity of DNA methyltransferases is an important mechanism that contributes to cancer. The reaction mechanism of DNA methyltransferases, which includes formation of a covalent intermediate between the enzyme and the target base, is the basis of the success of several anti-cancer drugs that are targeted against DNA methylation. These include 5-fluoro-2'-deoxycytidine, 5-aza-2'-deoxycytidine (Decitabine) and 2-H pyrimidinone-1-beta-D(2'-deoxyriboside) (Zebularine). This review provides an insight to how the chemistry of DNA methylation is involved in the performance of these drugs targeted against it.