Objective Velopharyngeal dysfunction (VPD) associated with 22q11.2 deletion syndrome (22q11.2DS) has a complex etiology. This study had 3 aims: (1) assess differences in velopharyngeal and levator muscle configuration during rest versus sustained speech production (2) compare differences in velopharyngeal changes between children with and without 22q11.2DS (3) examine the relationship between adenoid thickness, pharyngeal depth, and velopharyngeal changes. Design Cross-sectional. Methods A total of 22 participants, 11 with 22q11.2DS and 11 controls with normal speech and velopharyngeal anatomy (ages 4-12 years), underwent nonsedated MRI at rest and during sustained /i/. Differences in velar and levator muscle contraction across the 2 different conditions were analyzed, using matched paired t-tests. Mean differences across participant groups were examined. Correlation analyses were also conducted. Results When comparing differences between rest and sustained phoneme production (aim 1), significant ( P < .05) differences were noted for all velar and levator muscle variables. For differences in velopharyngeal changes between children with and without 22q11.2DS (aim 2), VP ratio and effective VP ratio were noted to be significantly different. Pharyngeal depth and adenoid thickness were correlated with velar and levator muscle change measures and ratios (aim 3). Conclusion Results from this study provide quantitative in vivo measurements of the contracted levator muscle and velum in young children with 22q11.2DS. Results demonstrated that VP ratio and EVP ratio are significantly different between children with and without 22q11.2DS and that pharyngeal depth is a strong clinical determinant of VPD in children with 22q11.2DS.