Mapping　of　genomic　DNA　methylation　is　a　dispensable　part　of　functional　genome.　We　have　developed　a　novel　method　based　on　methylation-specific　primer　and　serial　analysis　of　gene　expression,　called　MSP-SAGE　with　potential　of　high-throughput　quantification　of　genomic　DNA　methylation.　We　used　a　6-mer　methylation-specific　primer　to　extend　the　methylated　CpG　sequences　other　than　nonmethylated　CpG　sequences.　The　17　bp　tags　contained　methylated　CpG　sequence,　which　were　obtained　from　extended　methylation　sequence　by　digestion　of　restriction　endonuclease,　and　then　the　tags　were　concatenated　and　cloned　for　sequencing.　We　can　identify　the　locations　of　methylation　according　to　the　sequences　of　tags　and　quantity　the　methylation　status　from　the　frequency　of　the　tags.　MSP-SAGE　has　a　good　linearity　in　a　broad　rnethylation　range　from　5%　to　100%　with　good　accuracy　and　high　precision.　The　proof-of-principle　study　shows　that　MSP-SAGE　is　a　reliable　high-throughput　assay　for　quantification　of　DNA　methylation.　(c)　2006　Elsevier　Inc.　All　rights　reserved.