The role of gene body methylation, which represents a major part of methylation in DNA, remains mostly unknown. Evidence based on the CpG distribution associates its presence with nucleosome positioning and alternative splicing. Recently, it was also shown that cytosine methylation influences splicing. However, to date, there is no methylation-based data on the association of methylation with alternative splicing and the distribution in exonic splicing enhancers (ESEs). We presently report that, based on the computational analysis of the Human Epigenome Project data, CpG hypermethylation (>80%) is frequent in alternatively spliced sites (particularly in noncanonical) but not in alternate promoters. The methylation frequency increases in sequences containing multiple putative ESEs. However, significant differences in the extent of methylation are observed among different ESEs. Specifically, moderate levels of methylation, ranging from 20% to 80%, are frequent in SRp55-binding elements, which are associated with response to extracellular conditions, but not in SF2/ASF, primarily responsible for alternative splicing, or in CpG islands. Finally, methylation is more frequent in the presence of AT repeats and CpGs separated by 10 nucleotides and lower in adjacent CpGs, probably indicating its dependence on helical formations and on the presence of nucleosome positioning-related sequences. In conclusion, our results show the regulation of methylation in ESEs and support its involvement in alternative splicing.