Recently, it has been suggested that human herpesvirus-6 (HHV-6) may play a role in the pathogenesis of relapsing-remitting multiple sclerosis (RRMS), but there is not enough information related to the role of HHV-6 in secondary-progressive MS (SPMS). To address this question, we evaluated HHV-6 prevalence, active viral replication and viral load measured by quantitative real-time PCR, in DNA and mRNA extracted from peripheral blood mononuclear cells (PBMCs) and DNA extracted from serum; the samples were collected from 31 SPMS and 31 RRMS patients in a one-year follow-up study, and sex- and age-matched controls. The results were as follows: i) We found a statistical significant difference in HHV-6 DNA prevalences between RRMS and SPMS patients in: DNA extracted from PBMCs (P=0.027), DNA extracted from serum (P=0.010) and mRNA extracted from PBMCs (P=0.010). When we compared HHV-6 prevalences from RRMS patients in relapse and in remission with those from SPMS patients, we only achieved a statistical significance for the relapses (P=0.003 in DNA from PBMCs, and P<0.001 in DNA from serum samples and mRNA from PBMCs). ii) We only found HHV-6 variant A among HHV-6 positive samples in serum. iii) We did not find any difference in HHV-6 viral loads. These results suggest that HHV-6A does not play an active role in SPMS, while this virus may contribute to the pathogenesis of RRMS triggering MS attacks in a subset of patients.