A significant association was previously demonstrated between multiple sclerosis (MS) and the functional 5'-(GT)n polymorphism in the promoter region of the SLC11A1 gene, which has been implicated in both autoimmune and infectious disease susceptibility. In the present study the role of viral infection was investigated in South African MS patients in relation to specific SLC11A1 genotypes. Serum and peripheral blood mononuclear cells (PBMC) of 49 MS patients, 33 close relatives and 39 unrelated controls previously genotyped for SLC11A1 were screened for the presence of MS-associated retrovirus (MSRV) and two herpes virus (HHV-6 and EBV) sequences. Expression of the pol gene of MSRV was detected in the serum RNA of 34/49 (69%) MS patients whilst absent in the serum of 39 unrelated healthy control individuals (p < 0.001) but was also present in 23/33 (70%) of the unaffected close relatives of the patients. HHV-6 and EBV sequences were detected in both MS patients and control individuals. The viral sequences were not confined to a specific SLC11A1 genotype. Infection with these viruses is excluded as the primary cause for MS in the South African population since no significant differences were detected between MS patients and their unaffected close family members.