BACKGROUND: Muscle carnosine is related to contractile function (Ca++ handling) and buffering of exercise-induced acidosis. As these muscular functions are altered in Multiple Sclerosis (MS) it is relevant to understand muscle carnosine levels in MS. METHODS: Tibialis anterior muscle carnosine was measured in an animal MS model (EAE, experimental autoimmune encephalomyelitis, n = 40) and controls (CON, n = 40) before and after exercise training (EAEEX, CONEX, 10d, 1 h/d, 24 m/min treadmill running) or sedentary conditions (EAESED, CONSED). Human m. vastus lateralis carnosine of healthy controls (HC, n = 22) and MS patients (n = 24) was measured. RESULTS: EAE muscle carnosine levels were decreased (p < .0001) by ~ 40% to ~ 64% at 10d and 17d following EAE induction (respectively) regardless of exercise (p = .823). Similarly, human MS muscle carnosine levels were decreased (- 25%, p = .03). CONCLUSION: Muscle carnosine concentrations in an animal MS model and MS patients are substantially reduced. In EAE exercise therapy does not restore this.