•The interest in developing epigenetic drugs is substantially increasing.•We reviewed the recent epigenetics structure-activity relationships.•Epi-informatics has seen recent advances in databases and web servers.•Polypharmacology profiling is a must in the future of epigenetic drug discovery.•We briefly discuss the future directions of epi-informatics. The ability of epigenetic markers to affect genome function has enabled transformative changes in drug discovery, especially in cancer and other emerging therapeutic areas. Concordant with the introduction of the term ‘epi-informatics’, the size of the epigenetically relevant chemical space has grown substantially and so did the number of applications of cheminformatic methods to epigenetics. Recent progress in epi-informatics has improved our understanding of the structure–epigenetic activity relationships and boosted the development of models predicting novel epigenetic agents. Herein, we review the advances in computational approaches to drug discovery of small molecules with epigenetic modulation profiles, summarize the current chemogenomics data available for epigenetic targets, and provide a perspective on the greater utility of biomedical knowledge mining as a means to advance the epigenetic drug discovery. Epigenetic drug discovery is gaining growing attention both in industry and academia; ‘epi-informatics’ is an emerging concurrent area of computational research that helps accelerate this effort.