The aim of this prospective study was to describe the morphological and functional changes of the upper airways and the middle ears after rapid maxillary expansion (RME). Thirteen patients comprised the original study sample, of these three patients dropped out. Of the remaining 10 subjects, seven (two females, five males; average age, 8.7 years) underwent orthodontic RME with a Hyrax screw and three (one female, two males; average age, 8.3 years) served as the controls. Inclusion criteria for the study group were a uni- or bilateral crossbite with the evidence of a maxillary deficiency. Exclusion criteria were acute or chronic respiratory disease, allergies, cleft lip and palate, or absence of adenoids. An ear, nose, and throat (ENT) examination, lateral cephalometry, anterior rhinomanometry, tympanometry, and posterior rhinoscopy were carried out for each child at baseline (E1) and after 6 months (E2). Descriptive statistics were calculated for all diagnostic variables and correlations between the study and control group were evaluated. Rhinomanometry showed a correlation (r = 0.57) between the size of the nasal pharyngeal area and nasal airflow, but only at 150 daPa. The size of the adenoids measured on the lateral cephalograms was correlated with the endoscopic findings. The size of the adenoids remained the same after RME. Patients with maxillary constriction had the largest adenoids and showed a negative pressure in the middle ear. However, this was reduced after RME. The results suggest a possible impact of maxillary deficiency on otorhinological structures. RME may lead to otorhinological changes. Further interdisciplinary investigations are needed to corroborate these findings.