A systematic review was performed to analyze the current evidence on three-dimensional (3D) computed tomography (CT) superimposition protocols used to assess dentomaxillofacial changes after orthognathic and orthofacial surgery. Accuracy, reproducibility, and efficiency were evaluated./r/nThe search was divided into Main Search (PubMed, EMBASE, Cochrane Library, LILACS, and SciELO), Grey Literature search (Google Scholar and Open Grey), and Manual search. Thirteen studies were included. Of these, 10 reported data on accuracy, 10 on reproducibility and five on efficiency. Seven proposed or evaluated methods of voxel-based superimposition, three focused on the surface-based technique, one compared surface- and voxel-based superimposition protocols, one used the maximum mutual information algorithm, and one described a landmark-based superimposition method. Cone-beam computed tomography (CBCT) was the most common imaging technique, being used in 10 studies./r/nThe accuracy of most methods was high, showing mean differences smaller than voxels’ dimensions, ranging between 0.05 and 1.76 mm for translational accuracy, and 0.10-1.09° for rotational accuracy. The overall reproducibility was considered good as demonstrated by the small mean error (range: 0.01-0.26 mm) and high correlation coefficients (range: 0.53-1.00). Timing to complete virtual superimposition techniques ranged between a few seconds up to 40 min./r/nVoxel-based superimposition protocols presented the highest accuracy and reproducibility. Moreover, superimposition protocols that used automated processes and involved only one software were the most efficient.