Few investigations have evaluated the characteristics of functional and structural malocclusion in young children. Thus, the aim of this study was to assess the ultrasonographic thickness of the masseter and anterior portion of the temporalis muscles, the maximum bite force, and the number of occlusal contacts in children with normal occlusion and unilateral crossbite, in the primary and early mixed dentition. Forty-nine children (26 males and 23 females) was divided into four groups: primary-normal occlusion (PNO), mean (PNO) age 58.67 months; primary-crossbite (PCB), mean age 60.50 months; mixed-normal occlusion (MNO), mean age 72.85 months; and mixed-crossbite (MCB), mean age 71.91 months. Thickness was evaluated with the muscles at rest and during maximal clenching, and comparison was made between the right and left side (normal occlusion), and between the normal and crossbite side (crossbite). The results were analysed using Pearson's correlation, paired and unpaired t-test, and Mann-Whitney ranked sum test. The anterior temporalis thickness at rest was statistically thicker for the crossbite side than the normal side in the MCB group (P = 0.0106). A statistical difference in bite force and the number of occlusal contacts was observed between the MNO and MCB groups, with greater values for the MNO subjects (P < 0.05). Masseter muscle thickness showed a positive correlation with bite force, but the anterior temporalis thickness in the PCB and MCB groups was not related to bite force. Masticatory muscle thickness and bite force did not present a significant correlation with occlusal contacts, weight, or height. It was concluded that functional and anatomical variables differ in the early mixed dentition in the presence of a malocclusion and early diagnosis and treatment planning should be considered.