In this study we searched for genetic variation in a segment of the human endogenous retrovirus, HRES-1, which encodes a potential autoantigen of 28kDa. The purpose was to further investigate a possible association between this endogenous retrovirus and multiple sclerosis (MS). Fragments amplified from the HRES-1 region in question were subjected to single strand conformational analysis (SSCP analysis) and sequencing if the SSCP migration pattern suggested presence of polymorphisms. Using this approach a synonymous G → C substitution, creating an Ncil site, was found. Our sequence data also revealed an additional nucleotide in the region encoding the 28-kDa protein, i.e. a nucleotide not present in the first published sequence. This finding has implications for future studies of the 28-kDa HRES-1 protein since the additional nucleotide changes the reading frame of this protein. The detection of the Nci polymorphism allowed us to define a novel haplotype of HRES-1 distinct from the three previously known HRES-1 haplotypes. On comparison of the distribution of these four haplotypes in MS patients and healthy individuals we found a statistically significant difference (P = 0.03) but the contribution from the novel haplotype to this was modest.