Objective: To compare and assess the reproducibility of 3 methods for registration of maxillary digital dental models in patients with anterior open bite. Settings and sample population. Digital dental models of 16 children with an anterior open bite in the mixed dentition were obtained before (T1) and after 12 months of treatment with bonded spurs (T2). Methods: Landmarks were placed on all T2 models and 3 registration methods (R1, R2 and R3) were independently performed by 2 observers. R1 was based on 10 landmarks placed on posterior teeth. R2 was based on 5 landmarks on the palate (2 anterior, 2 posterior and 1 central). R3 used regions of interest around the 5 palatal landmarks used in R2. The differences between the registration methods were calculated by comparing the mean differences and standard deviations between the corresponding x, y and z coordinates of 6 corresponding landmarks in the T2 registered models. Repeated measures analysis of variance followed by post-hoc Bonferroni tests were used for comparisons (P <.05). The agreement between methods and the intra and interobserver reproducibility were assessed with Bland-Altman tests and intraclass correlation coefficients (ICC). Results: Comparisons of R2 with R3 methods showed greater agreement, mean differences ≤0.50 mm for all landmarks, than comparisons of R1 with R2, and R1 with R3, mean differences >0.50 mm for most of the y and z coordinates (P <.05). The R1 and R3 methods presented excellent intra and interobserver reproducibility and R2 method had moderate interobserver reproducibility. Conclusions: Longitudinal assessments of open bite treatment using digital dental models could consider the posterior teeth and/or the palate as references. The R1 and R3 methods showed adequate reproducibility and yield different quantitative results. The choice will depend on the posterior teeth changes and dental models’ characteristics.