The three-dimensional nature of scoliosis, coupled with changes due to natural history or treatment, is often difficult to quantify and visualise. A difference map was developed to compare the sequential surface topography of subjects over their treatment period. Three-dimensional surface maps representing patients' trunk surfaces were captured with a laser scanner. Patient surface maps from two clinic visits were matched using a manual best-fit technique that accounted for growth and positioning. The surfaces were subtracted, generating a colour-coded three-dimensional difference map displaying the surface changes. The difference maps were compared with known clinical measures, indicating good agreement (78% specific) with the clinical parameters in detecting change. Full agreement or agreement with the clinical parameters occurred in the surgical, brace and no treatment groups: 76%, 80% and 85%, respectively. A difference index (average of the absolute value of differences on a point-by-point basis) was calculated from the difference map, enabling quantification of change. The difference index, with zero being a perfect match, averaged 5 +/- 1 for repeated measures 7 +/- 2 for subjects deemed to have no change, 9 +/- 2 for subjects with slight change, and 14 +/- 2 for subjects with significant change. The difference map showed the extent and location of changes and is a useful tool for assessing surface topography changes.