Brain-specific proteins are biochemical markers of neurodegeneration. The aim of this study was to estimate the role of biomarkers in neuronal and glial damage as a potent marker of efficiency of immunosuppressive treatment. The levels of total Tau protein (tTau) and S100b protein were measured using the ELISA method in serum and cerebrospinal fluid (CSF) of 30 patients with RRMS, 24 patients with SPMS and 30 healthy subjects. Additionally, serum levels of tTau and S100b were assayed every 6 months during the 24-month mitoxantrone therapy. In CSF and serum of patients with MS, both tTau and S100b were increased compared to control group; however, no significant difference was found between respective MS types. In serum of mitoxantrone-treated patients, both proteins showed to decrease after 24 months, yet the difference was statistically significant only for S100b. CSF levels of tTau and S100b are elevated in patients with MS and can reflect an axonal and glial pathology. Measurement of serum concentrations of S100b may be useful for monitoring immunosuppressive therapy and may support clinical assessment. In contrast, tTau concentration did not prove to be a useful marker of mitoxantrone therapy.