Abstract Background This study compared the area and minimal section of the nasal cavity, nasopharynx, oropharynx, and hypopharynx in cases treated with different methods of microimplant-assisted expansion. Methods Based on a pilot study to calculate the sample size, 30 patients with transverse maxillary deficiency over 14 years of age were retrospectively selected. These patients had received two different types of microimplant-assisted maxillary expansion treatment (MARPE and BAME). The patient underwent Cone-Beam computed tomography (CBCT) before and after treatment (mean time 1.5 months) with MARPE or BAME and upper airway measurements (volume and minimum cross-sectional area) were taken to assess upper airways changes and compare changes between the groups. A paired sample t-test was performed to evaluate the T0-T1 change of airway measurements obtained with MARPE and BAME, and a student t-test to compare changes in airway measurements between MARPE and BAME. Results This investigation shows a statistically significant increase in total nasopharyngeal airway volume (0.59 ± 1.42 cm3; p