Changes in DNA methylation — one form of epigenetic regulation — are linked to a number of brain disorders. Here, Huynh et al. found differences in DNA methylation in pathology-free tissue from multiple sclerosis (MS)-affected and control brains. In the MS samples, several genes involved in oligodendrocyte survival were hypermethylated and their transcripts were downregulated. By contrast, several genes involved in proteolytic cleavage were hypomethylated and their transcripts were upregulated. These data suggest that DNA methylation may have a role in MS disease mechanisms.