Objectives: DNA cytosine methylation is a critical epigenetic modification involved in human diseases such as cancer and imprinting disorders. Various cellular processes including gene regulation, embryonic development, X chromosome inactivation, and chromatin remodeling are strongly associated with DNA methylation changes. Next-generation sequencing combined with sodium bisulfite treatment allows identification of methylation changes at single base resolution. However, whole genome bisulfite sequencing is prohibitively expensive. Additionally, many of the regions in whole genome bisulfite sequencing are in repetitive regions, and provide very little useful information. In many cases, the researcher is only interested in profiling a subset of biologically relevant regions. Methods: To address these needs, we have developed SureSelect Methyl-Seq, which combines Agilent’s SureSelect Target Enrichment platform with bisulfite sequencing to detect methylation changes. Our Methyl-Seq design targets human genomic CpG sites within CpG islands/shores, promoters, known differentially methylated regions (DMRs) and previously determined regulatory regions. Results: This comprehensive design covers 84Mb making it well suited to study cancer-, tissue-, and stem cell-specific DMRs. SureSelect Methyl-Seq can be also optimized for different sizes of custom designs. Conclusion: Here we describe the SureSelect Methyl-Seq workflow and demonstrate efficient target enrichment and precise methylation level detection. Further, we show high concordance with whole-genome bisulfite sequencing of known model systems. We also describe the detection of tissue and cancer specific DMRs.