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Objective. This study aimed to investigate the quality of cone beam computed tomography (CBCT) studies evaluating the effects of rapid maxillary expansion on upper airway morphology. Materials and Methods. A database search was conducted using PubMed, Ovid, and Cochrane Library up to December 2016. Studies in which CBCT was adopted to visualize the upper airway before and after rapid maxillary expansion were included. The population target was growing patients. Methodological quality assessment was performed. Results. The screening process resulted in the exclusion of 1079 references, resulting in only 9 remaining papers that fulfilled the inclusion criteria. No randomized clinical trials were found. The quality scores ranged from 36% to 68% of the maximum achievable, and the mean quality score of the studies was 50%. No good quality studies were detected in our sample. Conclusions. Inconsistencies in the CBCT protocols utilized were detected between studies. Head posture, tongue position, and segmentation protocols were not consistent. These discrepancies were reflected in the different results obtained in the studies. A valid and consistent protocol with regard to head and tongue positioning, as well as nasal cavity volume segmentation, is required.