Background: Multiple Sclerosis (MS) is a neurological condition that is partly characterised by T-cell mediated autoimmune dysfunction. Risk of developing MS is influenced by environmental and genetic factors. Genetic variation at the human leukocyte antigen (HLA) region incurs the greatest effect on MS yet there remains a large amount of unexplained genetic risk. Modifiable differences in DNA methylation are recognized as epigenetic contributors to MS risk and may provide a valuable link between environmental exposure and inherited genetic systems. Methods: We performed a genome-wide DNA methylation analysis of CD4+ T cells from 30 patients with relapsing remitting MS and 28 healthy controls using Illumina 450K methylation arrays. A step-wise prioritisation procedure was used to identify a panel of CpGs associated with MS in this cohort. Results: A striking differential methylation signal was observed at chr. 6p21, with a peak signal at HLA-DRB1. After prioritisation, we identified a panel of 74 CpGs (in 38 different genes) associated with MS in this cohort. Most notably we found evidence of a major effect CpG island in DRB1 showing an average of 26% hypomethylation in MS cases (PFDR<3´10-3). We also found evidence that methylation at this locus is partially influenced by the major MS risk haplotype DRB-1501* (P<005). In addition, we found 55 non-HLA CpGs that exhibited differential methylation, many of which localize to genes that have been previously linked to MS. Conclusion: Our findings provide the first evidence for association of DNA methylation at HLA-DRB1 in relation to MS risk. Further studies are now warranted to validate and understand how these findings are involved in MS pathology.