Patients with temporomandibular dysfunction (TMD) require antero-posterior (AP) correction of mandibular position inter alia. Determination of the limit of the AP correction using a sibilant phoneme registration (SPR) protocol is essential in not increasing muscular tonus. The aim of this study is to investigate the effect of a SPR protocol on the upper airway. Using acoustic pharyngometry data, mean airways of 46 adults undergoing treatment for TMD were reconstructed in 3-D and analyzed using finite element analysis and principal components analysis. When the mean baseline functional residual capacity (FRC) airway was compared to the mean collapsed residual volume (RV) airway, a 25% reduction in the 3-D upper airway was demonstrable (p < 0.01). When the mean baseline FRC airway was compared to the mean airway with SPR (FRC-SPR), a 12% increase was found at the oropharyngeal junction of the 3-D airway, but this finding failed to reach statistical difference. Similarly, when the mean FRC-SPR airway was compared to the mean RV-SPR airway, the amount of collapse was reduced to 16% but again no statistical difference was found. In contrast, when the mean RV airway was compared to the mean RV-SPR airway, a 15-18% increase was found (p< 0.05). It is concluded that the use of a SPR protocol may be useful in improving upper airway RV in patients, during treatment for TMD.