Histone proteins are subject to a diverse range of post-translational modifications which, along with DNA methylation, play a major role in controlling gene expression, cell division, survival and differentiation. Alterations in these chromatin modifications are thought to contribute to important human diseases including cancer. Inhibition of the enzymes that introduce and remove these chromatin modifications is proving an effective approach to cancer therapy and inhibitors of histone deacetylases and DNA methyltransferases have been approved for use in haematological malignancies. Here we provide a background to the biology of chromatin modifications and review some of the evidence validating histone deacetylases and DNA methyltransferases as targets for anti-cancer drug discovery. We then focus on two of the key issues in this field; the identification of novel inhibitors to overcome shortcomings of first generation agents and the potential role of histone deacetylase and DNA methyltransferase inhibitors in combination therapies for oncology. Finally, we highlight some of the challenges that will need to addressed to further progress the development of epigenetic-based therapies for cancer.