Next generation sequencing (NGS) technologies have catalyzed our ability to explore the influence of epigenetic modifications on economically important phenotypes of livestock. Towards this end, our goal was to gain insight into the extent of methylation in the bovine genome. To accomplish this, we have generated a protocol for producing genome-wide DNA methylation profiles via methyl binding domain sequencing (MBD-Seq). MBD-Seq is a technique that involves the sample enrichment of methylated genomic regions followed by their next-generation sequencing. Sequence reads were aligned to the UMD3.1 reference genome using NextGENe (SoftGenetics, State College, PA) software and methylation peaks were identified based upon the criterion of an average sequence coverage of 500X. Preliminary data indicate that several thousand methylated regions are located on every bovine chromosome. MBD-Seq libraries are currently being generated for liver, small intestine and longissimus dorsci muscle samples of 8 animals differing for residual feed intake (4 high and 4 low) and a methylation map of the bovine genome is being generated.