DNA methylation is associated with the silencing of gene expression. The predominant mechanism involves the methylation of DNA and the subsequent recruitment of binding proteins that preferentially recognize methylated DNA. In turn, these proteins associate with histone deacetylase and chromatin remodelling complexes to cause the stabilization of condensed chromatin. Recent studies have indicated that the opposite might also hold; namely, that targeting of methylation might depend on altered chromatin structure. The family of methyltransferases and methyl-binding proteins is expanding and becoming better characterized. This review will focus on the mechanisms of methylation-associated silencing of gene expression.