Torque teno virus (TTV) is highly prevalent in the general population worldwide. The relationship that TTV establishes with the central nervous system (CNS) of infected hosts is not clear but it is suspected that TTV infection of the CNS lead to increased local expression of inflammatory mediators that may play a role in the pathogenesis of multiple sclerosis (MS). The prevalence and load of TTV in serum and cerebrospinal fluid (CSF) of 207 MS patients and 93 age- and sex-matched healthy controls by qPCR designed on the untranslated region were analyzed. TTV DNA was not detected in CSF, TTV prevalence in serum was similar in MS patients (76.8%) compared to healthy controls (76.3%). Sub analyses performed in MS patients stratified on the basis of clinical phenotypes indicated that TTV viremia was significantly lower in individuals with relapsing remitting compared to chronic progressive disease. Notably, viremia was increased in primary progressive, compared to secondary progressive MS patients, and in relapsing remitting MS patients during quiescent compared to relapsing phases of disease. Since TTV interacts with toll-like receptor (TLR) stimulating the production of inflammatory cytokines, TLR9 expression were examined, showing that it was augmented on monocytes of chronic progressive MS patients, in whom higher TTV viremia was present, but this did not correlate with a distinct pattern of cytokine production. Overall these findings suggest that, although TTV infects the same proportion of MS patients and healthy controls, the levels of replication of the virus differ among patients, being correlated with the clinical phenotype of disease.