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Posterior crossbite is one of the most frequently occurring malocclusions in adolescents with a prevalence of 7% to 23%. The most common form of posterior crossbite is a unilateral posterior crossbite with a functional side shift. It has been suggested that functional posterior crossbites (FUPXB) may result in right-to-left-side differences in the condyle fossa relationship, resulting in temporomandibular joint (TMJ) problems. The objective of this study was to determine if pathological position of the condyles can cause condylar signs or symptoms like degenerative joint disease (DJD) or juvenile condylar resorption (JCR), or if the position of the condyle is just an altered position within the TMJ. Sixty patients with an average age of 9.6years were randomly selected from the office of one of the investigators (T.S.). The study group consisted of 29 patients with a FUPXB and the control group had 31 patients with no posterior crossbite. All patients had multislice CT scans of the TMJ taken as part of the orthodontic records. Transverse widths were measured at the skeletal base and the dentoalveolar base. Molar inclinations, condylar angulations, condylar anterior joint space, superior joint space, and posterior joint space were measured. Independent sample t-tests were used to compare different measurements between groups and paired sample t-tests were used to compare differences within the same patient. Reliability of measurements were determined using pairwise correlation. For dentoalveolar measurements of transverse width, the maxillomandibular difference for the study group was -8.2 mm and for the control group was -4.0 mm. No significant differences were found between the molar inclinations, condylar width, angulation, or any joint space measurements between the two groups. A total of 61.3% of the subjects in the control group and 72.4% in the study group had a radiographic sign of joint disease. The lack of condylar positional differences between the control and crossbite groups suggests that TMJ signs and symptoms in the study group may be related to remodeling in the TMJ instead.