Human endogenous retroviruses (HERVs) have been associated with multiple sclerosis (MS) pathogenesis. Several related HERV-W sequences have been implicated in disease occurrence and progression; the MS retrovirus (MSRV) is one such element whose envelope protein has been recently demonstrated to be involved in innate immune pathogenesis. To distinguish MSRV from other HERV-W sequences we analyzed the relative abundance of individual HERV-W env sequences by employing a real-time PCR approach using specific oligonucleotide primers and tissue samples from MS and non-MS patients. Our analyses reveal that ERVWE1 env-encoding DNA and RNA exhibited increased detection (p < 0.05) and expression (p < 0.01) in the brains of MS patients. Similarly, ERVWE1 env transcripts were inducible in glial cells (p < 0.05), while comparable changes in MSRV abundance were not observed. These results indicate that individual HERVs might have distinct roles in MS pathogenesis.