Unilateral posterior crossbite is a malocclusion disease that involves morpho-functional characteristics of masseter muscle; a normal or increased activity of contralateral muscle and a reduced activity of the ipsilateral muscle during unilateral crossbite have been shown. Since the extracellular matrix plays a key role in in mechano-transduction of transmitting forces during muscle contraction, the aim of the present study was to analyse the behaviour of extracellular matrix in this type of malocclusion through immunofluorescence reactions against laminin, collagen IV, MMP-2 and MMP-9. Our results show an increased expression of Laminin, Collagen IV, and MMP-9 in the contralateral side if compared to the ipsilateral side. No differences have been found in MMP-2 expression between contralateral and ipsilateral muscles. Since the increased expression of Laminin, Collagen IV and MMP-9 is associated with muscle hypertrophy and MMP-2 is associated with muscle atrophy, our results support the existence of a hypertrophic response of contralateral muscle during unilateral posterior crossbite that probably aims to compensate the altered function of the ipsilateral one.