The role of viral infections in multiple sclerosis (MS) pathogenesis is unclear. Certain neurotropic viruses previously linked with MS among white population were studied including Epstein-Barr virus, human herpesvirus-6 (HHV-6) and MS-associated retrovirus (MSRV). Sixty-two MS patients (37 had a recent clinical relapse) and 65 controls with other neurological disorders were included. Blood and cerebrospinal fluid (CSF) samples were obtained and processed with the primary objective of determining whether there was intrathecal multiplication of viruses under study (EBV, HHV6 A and B and human endogenous retrovirus) or a breach in blood-brain barrier associated with viral presence in both peripheral blood and CSF. Evidence of breach in blood-brain barrier was seen in 86.5% of patients as evidenced by abnormal CSF/serum albumin index and or MRI. EBV nuclear antigen (EBNA1 IgG) was seen in 89% of MS patients and 58% controls (P = <0.001). However, HHV6 IgG was similar in both groups (85% versus 81%; P = 0.45). In affinity immunoblotting reaction intrathecal IgG synthesis against EBNA1 antigen was demonstrable in 26% (16/62) of patients and none against HHV6. A subset of patients showed significant elevation in mean copy number of plasma EBV DNA during relapse and there was a trend for the same among patients harboring HHV-6B. No evidence of isolated intrathecal viral presence or multiplication was seen. The results of our study suggest that viruses studied namely EBV and HHV6 have a role in triggering relapses through a peripheral mechanism, rather than a direct role through intrathecal multiplication.