BACKGROUND: The pathogenesis of relapsing-remitting multiple sclerosis (RRMS) is linked to autoimmune attacks against myelin proteins, and reactivation of Epstein-Barr virus (EBV) and human herpesvirus 6 (HHV-6). However, the connection between viral reactivation and autoimmune biomarkers has remained unclear. OBJECTIVES: To investigate immunoglobulin (Ig)G/IgA/IgM responses targeting myelin-related proteins in association with EBV and HHV-6 replication markers in RRMS. METHODS: We recruited 55 patients with RRMS and 63 healthy controls and assessed IgG/IgA/IgM responses against seven myelin-related components, as well as EBV nuclear antigen 1 (EBNA-1) and deoxyuridine-triphosphate nucleotidohydrolase (dUTPases). Disability was evaluated using the Expanded Disability Status Scale (EDSS) and disease progression using the Multiple Sclerosis Severity Score (MSSS). RESULTS: IgG/IgA/IgM levels targeting seven myelin-related proteins were significantly higher in RRMS than in controls. IgG against myelin basic protein (MBP) (IgG-MBP), IgM-myelin-associated glycoprotein (IgM-MAG)-37-60, IgA-MBP, and IgA-myelin-oligodendrocyte-glycoprotein (IgA-MOG-31-55) distinguished RRMS from controls with a predictive accuracy of 96.6 % (sensitivity = 95.7 %, specificity = 95.2 %) and an area under the ROC curve of 0.991. A large part of the variance in the EDSS (around 75 %) and MSSS score (62.8 %) was explained by IgG-MBP, IgM-MBP, IgA-MOG-31-55, and IgM-MAG. Part of the variance (47.4 %) in the IgG/IgA/IgM responses to myelin-related proteins was explained by immune responses to EBNA and dUTPases of EBV and HHV-6. CONCLUSIONS: Autoimmune reactivities targeting myelin-related proteins are valuable biomarkers of RRMS and the severity and progression of RRMS. Reactivation of EBV and HHV-6 may trigger or maintain these autoimmune responses thereby impacting disease progression.