The objective of this study was to examine if chin cup therapy have any adverse effect on the sagittal pharyngeal dimensions in Class III malocclusion patients. Twenty patients (10 girls and 10 boys; mean age 10.31 +/- 1.15 years) with skeletal Class III malocclusion, and an untreated control group (8 girls and 10 boys, mean age 9.89 +/- 1.55 years) were evaluated. The chin cup appliance and an occlusal bite plate with 600 grams totally was used for 9.78 +/- 0.93 months. Linear, angular and area measurements were evaluated on the cephalometric radiographs taken before and after observation and treatment periods. Treatment changes showed significant increases in maxillary forward position, effective length of the maxilla and the mandible, and vertical facial height measurements. The mandible showed a clockwise rotation revealed by the decrease in SNB and the increase in mandibular plane angles. Significant increase in the nasopharyngeal area was found when the treatment and control groups were compared. The nasopharyngeal airway area was affected by chin cup treatment, without any adverse effect on the pharyngeal airway dimensions in the short term.