mTOR has been shown to be involved in the regulation of immune responses and differentiation of immune cells. This protein is a candidate molecule for unraveling the molecular mechanisms of autoimmune disorders such as multiple sclerosis (MS). We designed the current study to assess expression of MTOR, and four associated long non-coding RNAs (lncRNAs), namely SNHG1, SNHG3, SHNG5 and DANCR in the peripheral blood of patients with MS compared with healthy controls. Analysis of real-time PCR results has shown down-regulation of SNHG5 and DANCR in MS patients compared with controls. Sex of study participants had no significant effect on expression of either genes and the interaction of sex and disease on expression levels of all studied genes were insignificant. There was a significant negative correlation between expression levels of MTOR gene and disease duration. No other significant correlations were detected between genes expressions and clinical/demographic data. SNHG5 and DANCR transcript levels had AUC values of 0.88 and 0.68 in separation of patients with MS from healthy controls, respectively. Taken together, our study suggests participation of two mTOR-related lncRNAs, i.e. SNHG5 and DANCR in the pathophysiology of MS.