The purpose of this study was to investigate the stability of the medial aspects of the rugae in patients where rapid maxillary expansion (RME) was performed in addition to fixed appliance therapy. Nineteen subjects that met the inclusion criteria for each group were randomly selected from the archive of one orthodontist office. The RME/fixed appliances group consisted of 8 males and 11 females (mean age pre-treatment 12.4 +/- 2.0 years). The control group treated with fixed appliances only, consisted of 6 males and 13 females (mean pre-treatment age of 12.5 +/- 2.1 years). The medial aspects of the rugae were recorded on the pre- and post-treatment dental models by means of a standardized photographic set-up. The transverse and antero-posterior positional rugae changes were measured. Kolmogorov-Smirnov normality tests were performed and paired t-tests were used to determine differences between and within the groups. The addition of RME to fixed appliance therapy caused a change in transverse measurements between the medial aspects of the bilateral rugae. There was no change in antero-posterior measurements (APM). The transverse changes were more marked for the third, less for the second rugae, and the least for the first rugae. The medial aspects of the third rugae cannot be considered as stable reference landmarks for dental cast analysis when RME is performed in addition to fixed appliance therapy.