Methods for tracking gum line changes by comparing digital 3D models of teeth and gingiva taken at different times. The digital 3D models are segmented to digitally identify the teeth from the gingiva, and the segmented digital 3D models are compared to detect gum line changes by determining differences between them relating to the gum line. Gum line changes can also be estimated by comparing one of the digital 3D models with a 3D model having a predicted original location of the gum line. Gum line change maps can be displayed to show the gum line changes determined through the tracking or estimating of changes. The digital 3D models can also be displayed with periodontal measurements placed upon them.