Multiple sclerosis (MS) is an inflammatory disease of the central nervous system. There are many types of disease-modifying drugs available but none of them can cure MS. The studies reported in this thesis analyzed the changes which happen at the transcriptome level during the course of treatment with glatiramer acetate (GA) and interferon-beta-1b. The studies reported revealed several differentially expressed transcripts which included both mRNAs and microRNAs. These can be considered as biomarkers for therapy monitoring and help to better understand the mechanisms of action of the drugs.