Pharyngeal residue, the material that remains in the pharynx after swallowing, is an important marker of impairments in swallowing and prandial aspiration risk. The goals of this study were to determine whether the 2D area of post-swallow residue accurately represents its 3D volume, and if the laterality of residue would affect this association. Thirteen patients with dysphagia due to brainstem stroke completed dynamic 320-detector row computed tomography while swallowing a trial of 10 ml honey-thick barium. 3D volumes of pharyngeal residue were compared to 2D lateral and anterior-posterior areas, and a laterality index for residue location was computed. Although the anteroposterior area of residue was larger than the lateral area, the two measures were positively correlated with one another and with residue volume. On separate bivariate regression analyses, residue volume was accurately predicted by both lateral (R2 = 0.91) and anteroposterior (R2 = 0.88) residue areas, with limited incidence of high residuals. Half of the sample demonstrated a majority of pharyngeal residue lateralized to one side of the pharynx, with no effect of laterality on the association between areas and volume. In conclusion, the area of post-swallow pharyngeal residue was associated with volume, with limitations in specific cases. Direct measurement of pharyngeal residue volume and swallowing physiology with 3D-CT can be used to validate results from standard 2D instrumentation.