The objective of the present study was to analyze morphological aspects of the structures of the stomatognathic system and their relationship with malocclusion. For this purpose, we determined the morphological alterations that occur in the masseter muscle of guinea pigs (Cavia porcellus) after the induction of malocclusion by extraction of the left upper molars. Animals were divided into two groups (malocclusion and control group) and submitted to macroscopic, biometric and light microscopic analyses. The results showed a reduction in the width of the masseter muscle mainly in left side in the malocclusion group 60 days after unilateral extraction. Microscopically, round and polygonal muscle fibers of several diameters were observed, and altered muscle fibers with a central nucleus, degenerating fibers and macrophages were noted in more deeply fasciculi