The analysis of the masticatory muscle activity in subjects with altered occlusal relationships could provide useful data of the functional impact of morphological discrepancies. Thirty subjects aged 16-18 years, with a sound, full permanent dentition, bilateral angle class I, and an overjet and overbite between 2 and 5 mm, were examined. The control group (10 male, 10 female) had no crossbite, while the crossbite group (four male, six female) had a posterior unilateral crossbite (five on the left side, five on the right side). The electromyographic activity of the left and right masseter and temporalis anterior muscles was recorded during 15 s of unilateral (left and right) chewing of gum, and expressed as a percentage of the maximum voluntary clench on cotton rolls. For each subject, the masticatory frequency, the confidence ellipse of the simultaneous differential left-right masseter and temporal activity (Lissajous figure), and an index of muscular symmetry, were computed to assess muscular coordination. In the crossbite subjects, the four analysed muscles appeared to contract with altered and asymmetric patterns. A large variability was found, and the confidence ellipses calculated for the chewing tests performed on the crossed sides were not significant, while the confidence ellipses of the uncrossed side chewing were different from the ellipses computed in the normal occlusion group. The altered occlusal relationship influenced the coordination of the masticatory muscles during chewing on both sides. The functional alteration was more apparent when the side with the altered morphology was directly involved, i.e. when chewing was performed on the crossbite side.