This article is available from: http://www.biomedcentral.com/1471-2164/8/252[Background] Epigenetic regulators (histone acetyltransferases, methyltransferases, chromatinremodelling enzymes, etc) play a fundamental role in the control of gene expression by modifying the local state of chromatin. However, due to their recent discovery, little is yet known about their own regulation. This paper addresses this point, focusing on alternative splicing regulation, a mechanism already known to play an important role in other protein families, e.g. transcription factors, membrane receptors, etc.[Results] To this end, we compiled the data available on the presence/absence of alternative splicing for a set of 160 different epigenetic regulators, taking advantage of the relatively large amount of unexplored data on alternative splicing available in public databases. We found that 49 % (70 % in human) of these genes express more than one transcript. We then studied their alternative splicing patterns, focusing on those changes affecting the enzyme's domain composition. In general, we found that these sequence changes correspond to different mechanisms, either repressing the enzyme's function (e.g. by creating dominant-negative inhibitors of the functional isoform) or creating isoforms with new functions.[Conclusion] We conclude that alternative splicing of epigenetic regulators can be an important tool for the function modulation of these enzymes. Considering that the latter control the transcriptional state of large sets of genes, we propose that epigenetic regulation of gene expression is itself strongly regulated by alternative splicing.The authors are grateful to the SwissProt team for their support. XdC acknowledges funding from the Spanish government (grants BIO2003- 09327, BIO2006-15557). MM-B and NB acknowledge funding from the Spanish government (grants SAF2002-00741, SAF2005-01285, Gen2003- 20642, CSD2006-00049, and BFU2006-01493/BMC). NB acknowledges financial support from the Parc Científic de Barcelona. SL acknowledges financial support from the Consejo Superior de Investigaciones Científicas.Peer reviewed