Unilateral posterior crossbite is a type of malocclusion that involves morpho-functional characteristics of masticatory muscle, such as the masseter: electrophysiological data have shown that the affected side works less than the contralateral muscle, which shows a normal or increased activity, probably in order to compensate for the affected side. The aim of present work was to measure the diameter and the cross-sectional area of ipsilateral and contralateral muscle fibers to verify if hypertrophy and/or hypotrophy take place in this malocclusion. We used immunofluorescence pictures to measure, using ImageJ software, the diameter and the cross-sectional area of fibers from control and crossbite groups; after that, the data were processed to perform statistical analyses. Results show that the fiber diameters of contralateral muscle are larger than the diameters of ipsilateral and control fibers, and that this difference is statistically significant. No statistically significant difference was found between the fiber diameters of the ipsilateral and control muscles. All these data suggest that, during unilateral posterior crossbite, morphological changes take place in the contralateral masseter muscle, which undergoes hypertrophy, probably to compensate for the low activity of the affected muscle.