INTRODUCTION: The aim of this study was to 3-dimensionally assess the treatment outcomes of bone-anchored maxillary protraction (BAMP) in patients with unilateral cleft lip and palate. METHODS: The cleft group comprised 24 patients with unilateral cleft lip and palate and Class III malocclusion with mean initial and final ages of 11.8 and 13.2 years, respectively. The noncleft group comprised 24 noncleft patients with Class III malocclusion with mean initial and final ages of 11.9 and 12.9 years, respectively. Cone-beam computed tomography examinations were performed before and after BAMP therapy in both groups and superimposed at the cranial base. Three-dimensional displacements of maxillary landmarks were quantified and visualized with color-coded maps and semitransparent superimpositions. The t test corrected for multiple testing (Holm-Bonferroni method), and the paired t test was used for statistical comparison between groups and sides, respectively (P <0.05). RESULTS: BAMP produced anterior (1.66 mm) and inferior (1.21 mm) maxillary displacements in the cleft group with no significant differences compared with the noncleft group. The maxillary first molars of the cleft group showed significantly greater medial displacement than did those in the noncleft group. The zygoma showed significantly greater lateral displacement at the cleft side compared with the noncleft side. CONCLUSIONS: BAMP caused similar amounts of maxillary protraction in patients with and without unilateral cleft lip and palatem with discrete differences between the cleft side and the noncleft side.