Objective: The aim of this study was to evaluate craniofacial asymmetry in children with transverse maxillary deficiency, with or without functional unilateral posterior crossbite (UPC), before and after rapid maxillary expansion (RME). Setting and sample population: A sample of 51 children with cone beam computed tomography scans obtained before RME (T1) and a year after RME (T2). Material and methods: This prospective study consisted of 2 groups: 25 children with functional UPC (6.77 ± 1.5 years) and 26 children without UPC (7.41 ± 1.31 years). Linear and angular measurements were obtained from zygomatic, maxilla, glenoid fossa and mandible, using original and mirrored 3D overlapped models. All right and left side comparisons in both groups and intergroups asymmetries were compared using MANOVA and t test for independent samples, respectively, statistically significant at P < .05. Results: The UPC group showed no side differences, but mandibular horizontal rotation at T1, and this asymmetry was improved in T2. The non-UPC group showed at baseline significant lateral asymmetry in orbitale, position of palatine foramen, respectively, in average 2.95 mm and 1.16 mm, and 0.49 mm of average asymmetry in condylar height. The glenoid fossa was symmetric in both groups at T1 and T2. Conclusions: Children with transverse maxillary deficiency showed slight morphological asymmetry, located in the mandible position in cases of UPC, and in the orbital and maxillary regions in cases without UPC. One year after RME, patients improved their craniofacial asymmetry, with significant changes in the mandible and correction of the mandibular rotation in patients who presented UPC.