This protocol describes methylation mapping analysis by paired-end sequencing (Methyl-MAPS). In addition to the sequence information, paired-end sequencing provides information about the physical distance between the two reads in the genome. Methyl-MAPS typically samples ~80% of the CpG dinucleotides in the genome and is also able to report the methylation status of individual genomic loci harboring repetitive elements. This is achieved by enzymatic fractionation of the genome into methylated and unmethylated compartments. Because the method avoids the use of bisulfite modification, DNA fragments of relatively large size are preserved, permitting the generation of paired-end libraries with DNA inserts of known size in the ranges of 0.8–1.5, 1.5–3, and 3–6 kb. The paired-end configurations can be uniquely mapped to the genome in most instances, because the paired reads will span most repetitive element sequences.