For the treatment of localised masticatory muscle pain, it is still unknown whether exercises have any efficacy. The understanding of these supposed biological effects is linked to the pathophysiological model of localised myofascial pain and dysfunction (MPD). (1) Motor activity: In MPD, the pain adaptation model implies that there is an agonist-antagonist co-activation. In healthy muscles, training exercises allow a tendency to a switch from agonist-antagonist co-activation towards reciprocal inhibition, either during isometric contractions or during isokinetic contractions. (2) Hemodynamics: In MPD, a hypoperfusion is supposed. In healthy muscle, training exercises enhance the functional hyperaemia.(3) Histology: (a) In females with localised trapezius myalgia, but not in males, there is a decrease in capillarisation. Exercises induce capillary angiogenesis in healthy muscles, and also in females with trapezius myalgia. (b) In myalgic females, but not in males, there is a tendency towards a higher proportion of type I fibres; exercises decrease the proportion of type I fibres, with a reciprocal increase of type IIA fibres (phenotypic conversion). (4) Biochemistry: There may be a cytochrome c oxidase (COX) deficiency that could explain the lower ATP concentrations in female patients. Exercises induce a decrease in the proportion of COX-negative fibres. Finally, a 10-week training program might have specific positive effects. Physiological mastication could be both a natural means of re-education and one of the goals of treatment.