The aim of the present study was to develop a 3D digital image-analysis method to quantitatively assess gingival changes after clear-aligner orthodontic therapy. Using teeth as fixed reference points, 3D image analysis tools have been used to quantify mucosal level changes after specific therapies. This technology has not been applied to orthodontic therapy, primarily because orthodontic tooth movement precludes using teeth as fixed reference points. Rather than superimposing the pre- and posttherapy volumes for the entire dentition, the methodology presented herein superimposed the pre- and post-therapy volumes for individual teeth. The lingual tooth surfaces, which remained unaltered, were used as fixed references. Intraoral scans taken before and after clear-aligner orthodontic therapy were imported for comparison. Volumes were created for each 3D image and were superimposed in a 3D image-analysis software that allowed quantitative measurements. The results demonstrated this technique's ability to measure very small changes in the apicocoronal position of the gingival zenith, as well as alterations of gingival margin thickness, following clear-aligner orthodontic therapy. The present 3D image-analysis method offers a useful tool for investigating the periodontal dimensional and positional changes that accompany orthodontic therapy.