Methods for the purification of enveloped HHV-6 virions and the viral DNA are presented. The viral genome is estimated to be 170,000 base pairs in size and does not appear to contain inversions due to absence of submolar bands by restriction enzyme analyses. The genomes of two independent HHV-6 isolates, HHV-6GS and HHV-6Z29, showed restriction enzyme site pleomorphism. Large scale purification of enveloped HHV-6 was achieved by continuous flow centrifugation utilizing sucrose gradients, DNAse 1 treatment and banding on 10-30% Dextran T10 gradients. The viral proteins were visualized on high resolution two dimensional polyacrylamide gels and the proteins recognized by serum antibody from patient GS were detected by HR2D Western blot analysis and radioimmunoprecipitation assay. The major antigenic proteins were 200, 120, 80, 72, 30 and 19 kDa.