BACKGROUND This study was undertaken in order to investigate the possible relation of HHV-6 and EBV in relapsing-remitting MS (RRMS). METHODS A one-year follow up study was performed analysing peripheral blood mononuclear cells and serum samples of 57 patients with RRMS and 57 healthy blood donors (HBD) by a quantitative real time PCR, to detect HHV-6 and EBV. Clinical data (starting age and EDSS increase) were collected. RESULTS We did not find any statistically significant difference for EBV between RRMS patients and HBD. Regarding HHV-6: i) There was a higher prevalence of HHV-6 in RRMS patients than in controls: 80.7% versus 29.8% respectively. ii) HHV-6 active replication seems to be related to exacerbations. iii) Only variant A was detected among RRMS patients with HHV-6 active replication. iv) Although some difference was found when we compared clinical data in RRMS patients with and without HHV-6 active replication, the results did not reach statistical significance. CONCLUSIONS A higher HHV-6A frequency of active infection (reactivation or new infection) would lead to a more frequent exposure of HHV-6A antigens to the immune system of RRMS patients; this active replication of HHV-6A seems to be specifically related with the exacerbations in a subset of RRMS patients.