Objective: To evaluate the changes in pharyngeal airway dimensions and the position of the hyoid bone after maxillary protraction with different alternate rapid maxillary expansion and construction (Alt-RAMEC) protocols in patients with skeletal class III malocclusion as a result of maxillary retrusion. Material and Methods: The patients with skeletal class III malocclusions were consecutively divided into two groups. Group 1 consisted of 17 patients (11 boys and 6 girls, mean age 11.31 6 1.71 years) who had the Alt-RAMEC protocol for 5 weeks, and group 2 consisted of 17 patients (10 boys and 7 girls, mean age 11.64 6 1.24 years) who had the Alt-RAMEC procedure for 9 weeks. In this study, 4 angular and 13 linear measurements were performed to evaluate the skeletal and pharyngeal airway changes that occurred after maxillary protraction. Results: A significant increase in the maxillary growth, inhabitation of mandibular growth, and clockwise rotation of the mandible caused the improvement of the maxillo-mandibular relationship in both groups. Those changes caused a significant increase in the upper pharyngeal airway dimension (P , .01) and affected the vertical position of the hyoid bone in both groups (P , .05 and P , .01, respectively). However, changes that occurred in both groups were found to be similar for all airway variables (P . .05). Conclusion: Upper pharyngeal dimension and vertical position of the hyoid bone were affected by the maxillary protraction with different Alt-RAMEC protocols. There were no statistically significant differences between the groups. (Angle Orthod. 2017;87:519-525)