Multiple Sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) with unpredictable clinical outcome. As such, there is an urgent need to identify biomarkers that can predict the treatment response. Therefore, in an open-label, clinical, paraclinical and molecular prospective study, we assessed 50 interferon (IFN) treated MS patients for Rio Score (RS)/Modified Rio Score (MRS) and densitometric expression of the interferon-induced protein 35 (IFI35), a signal-protein with potential to be clinically relevant in the management of the disease. We found 4.92-fold upregulated IFI35 in IFN-treated MS group respect to healthy controls (p < .0001) and 2.31-fold respect to untreated MS group (p < .0001). Moreover, IFI35 expression profile correlated with RS and MRS rank values (r = -0.6018, p < .0001; r = -0.620, p < .0001), white matter volume (r = -0.5041; p = .0017) and cerebral lesion load (r = -0.5075; p = .0026). Finally, the main proportion of IFN-treated MS patients non-reaching the 65% threshold in IFI35 expression leaved the RS/MRS rank value 0 in a period ranging from 5 to 15 months (p < .0001) from the study entry; instead, all patients that reaching this threshold maintained the RS/MRS value 0 until the study end (p < .0001). In conclusion, the expression level of IFI35 in untreated MS patients highlights a correlation with neuroinflammation. Furthermore, IFI35 expression in IFN-treated MS patients shows a modular correlation between dosing regimes, which is predictive for long-term clinical outcome and drug efficacy.Copyright © 2020. Published by Elsevier Inc.