OBJECTIVES: Multiple sclerosis (MS) onset risk factors include Epstein-Barr virus (EBV) indices (including host response), lower serum 25-vitamin D (25(OH)D) levels, low sun exposure, and HLA-DRB1*1501. The underlying molecular mechanisms are unclear. Here, we examined mediation through differential DNA methylation (DNAm) to better understand possible epigenetic programming. METHODS: Two case-control studies (Ausimmune Study, Australia = 206 cases + 348 controls; and Epidemiologic Investigations of MS [EIMS], Sweden = 140 cases + 139 controls). DNAm was measured using Illumina arrays. Dimension-reduction methods generated MS-associated DNAm modules. Pathway enrichment analyses were used to describe DNAm modules' system-level biological characteristics. Individual and joint associations with MS risk were assessed using logistic regression. DNAm module mediation of risk factor-outcome associations were assessed using mediation analysis. A range of temporality analyses were used. RESULTS: EBV indices (infectious mononucleosis history and anti-EBNA IgG titer), lower 25(OH)D, low sun exposure, and HLA-DRB1*1501 risk variant were individually and jointly associated with MS risk. In each study, 2 DNAm modules were found which mediated multiple exposure-MS associations. Proportions mediated ranged from 21 to 47% in Ausimmune and 25 to 53% in EIMS. Results were robust to sensitivity analyses. Top-ranked genomewide association study (GWAS) MS risk-associated genes were over-represented in both Ausimmune DNAm modules, A1 3.5-fold (p = 0.004) and A2 3-fold (p = 0.015). Reactome pathways enriched for DNAm had cross-study overlap - 45% of pathways enriched in Ausimmune DNAm modules were also enriched in EIMS (4.82-fold, p < 0.001). INTERPRETATION: EBV, lower vitamin D, low sun exposure, and HLA-DRB1*1501 risk variant act in concert and through common epigenetic pathways to impact MS onset risk. ANN NEUROL 2026;99:341-355.