Human herpesvirus 6 (HHV-6) has been linked to the pathogenesis of multiple sclerosis (MS). Based on antibody detection and quantitative HHV-6 polymerase chain reaction assay, this study aimed to analyze the possible association between infection with HHV-6 and MS. A total of 131 serum samples were analyzed by ELISA for the presence of specific antibodies to HHV-6 latency-associated U94/REP protein: 68 serum samples from 60 MS patients (20 in relapse and 48 in remission phase) and 63 serum samples from 63 healthy controls. Real-time quantitative PCR for HHV-6 U94/rep DNA was also performed in total blood of MS patients and healthy controls. The serological analysis by ELISA showed that MS patients had increased prevalence and titers of anti-U94/REP immunoglobulins in comparison with control group (seroprevalence 51.47 % versus 28.57 % and mean titer of positive samples 1:248 versus 1:110; p=0.0005), with significant difference between relapse and remission phases. HHV-6 DNA was detected in 4 of 60 MS patients (6.66 %) and in 2 of 63 healthy controls (3.17 %), confirming previous data of prevalence obtained by qualitative nested PCR. However, viral load was higher in MS patients compared to controls, and differences were statistically significant (p=0.02). The results show that, in spite of the low presence of HHV-6 DNA in peripheral blood, MS patients have increased prevalence and titer of IgGs reacting with HHV-6 latency-associated U94/REP protein.