Multiple sclerosis (MS) is considered as an autoimmune disease with expanding axonal and neuronal degeneration in the spinal cord or cerebral cortex during the acute MS phase. The hypothalamus (HYP) is often overlooked yet controls important homeostatic functions. This 1H MRS study performed on 1.5 T MR scanner using 3D CSI with 10×10×12.5 mm3 voxels was focused to altered HYP metabolism in early MS. Considering our results, increased Glx ratios with reduced mIns and tNAA ratios in HYP suggested glutamate excitotoxicity associated with glial activity and neuronal damage. This indicated that HYP plays an important role in early disease evolution.