The high-dose IFNa therapy is widely used for the treatment of hepatitis C, hematological malignancies, multiple sclerosis etc, and accompanied by side effects with largely undefined mechanisms of IFNa neurotoxicity. We applied self-elaborated tool COTRASIF (conservation-aided transcription-factor-binding site finder) for genome-wide bioinformatical search in rat and mouse genome for genes containing in their promoters IFN-stimulated response elements (ISRE) and discovered new putative target genes of IFNa, which encode the proteins involved in chemical synaptic transmission in central nervous system. The goal of the study is to verify the bioinformatical prediction and to find out the means to alleviate the IFNa therapy side effects on the basis of newly discovered and experimentally confirmed target genes of IFNa in central nervous system.