Multiple sclerosis (MS) is a chronic autoimmune disease that affects the central nervous system (CNS). In its early stages, it results in inflammation, demyelination, and axonal loss. Egypt has the highest rates in the Middle East region. The pathogenicity of MS involves mitochondrial function. Damage to mitochondrial DNA (mtDNA) can produce variation in the copy number (CN) and decline in mitochondrial function. Our goal was to determine the potential of mtDNA-CN as a biomarker of MS and the progression of the disease. The study included 25 patients with relapsing remitting MS (RRMS) and 25 age and sex matched apparently healthy control. Two peripheral blood samples were collected from each patient, one during the remission phase and the other during the phase of relapse. A quantitative real-time polymerase chain reaction (qPCR) was performed to assess CN of mitochondrial DNA. There was a statistically significant decline in the number of mtDNA copies during the remission phase as compared to controls (p<0.01), yet no difference was seen between mtDNA-CN in relapsing subjects versus controls. Moreover, the copy number of mtDNA during the relapse phase was significantly higher than the remission phase suggesting the ability of mtDNA to differentiate between remission and relapse phases (p<0.05). Our study observed that mtDNA-CN at a cut off (0.75), can differentiate between RRMS patients in the remission phase and controls with a sensitivity of 56%, specificity 84%, positive predictive value (PPV) 65.6% and negative predictive value (NPV) 77.8%, and at a cut off (1), mtDNA-CN can differentiate between remission and relapse MS patients with a sensitivity 72%, specificity 56%, PPV 62.1% and NPV 66.7%. In conclusion, mtDNA-CN can be proposed as a biomarker of MS.