Background: Multiple sclerosis (MS) has been considered a T cell–mediated autoimmune demyelinating disorder. Nuclear factor κB (NF-κB) is one of the master transcription factors that regulate the activity of inflammatory cells the present study aimed to investigate the NFKB/P65 mRNA levels in patients with MS and to assess its role in the prediction of Hashimoto’ thyroiditis (HT). Methods: 50 patients with clinically definite relapsing-remitting multiple sclerosis (according to the McDonald criteria 2017) compared to 50 healthy age and sex-matched controls. Thyroid serum antibodies, IgG index (IgG), and oligoclonal band (OCB) were assessed. The relative expression of NFKB/P65 mRNA was measured using real-time quantitative PCR. Results: there were significantly higher values of NFKB/P65 mRNA levels in patients with HT (2.4±0.54) compared to other patients without HT (1.3±1.45) and control group (0.8±0.17), p <0 .001. Significant associations were confirmed between NFKB/P65 mRNA correlated to thyroid autoimmunity and MS manifestations, p <0. 001. Linear regression revealed that only FT4 and TSH were independent variables correlated with NFKB/P65 mRNA, p < 0.001. Regarding prediction of MS, ROC curve revealed that the sensitivity of NFKB/P65 mRNA was 96 %, and specificity was 88% at cutoff 0.98 with (95% CI = 0.909–0.999). Concerning HT prediction, the cutoff 1.42 with (95% CI = 0.843–1.000)with a sensitivity of 93.8 % and, a specificity of 87.4%. Conclusions: NFKB/P65 mRNA increased in patients with MS more specifically in HT. Thus, NFKB/P65 mRNA could be used as noninvasive prediction markers of MS and HT. Keywords: Hashimoto’ Thyroiditis; Multiple Sclerosis; oligoclonal band; Nuclear factor κB; thyroid peroxidase.