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To investigate biomechanical effects of cleft type (unilateral/ bilateral cleft lip and palate), facemask anchorage method (tooth-borne and miniplate anchorage), and alveolar bone graft on maxillary protraction.Three-dimensional finite element analysis with application of orthopedic force (30° downward and forward to the occlusal plane, 500 g per side).Computed tomography data from a 13.5-year-old girl with maxillary hypoplasia.Eight three-dimensional finite element models were fabricated according to cleft type, facemask anchorage method, and alveolar bone graft.Initial stress distribution and displacement after force application were analyzed.Unilateral cleft lip and palate showed an asymmetric pattern in stress distribution and displacement before alveolar bone graft and demonstrated a symmetric pattern after alveolar bone graft. However, bilateral cleft lip and palate showed symmetric patterns in stress distribution and displacement before and after alveolar bone graft. In both cleft types, the graft extended the stress distribution area laterally beyond the infraorbital foramen. For both unilateral and bilateral cleft lip and palate, a facemask with a tooth-borne anchorage showed a dentoalveolar effect with prominent stress distribution and displacement on the upper canine point. In contrast, a facemask with miniplate anchorage exhibited an orthopedic effect with more favorable stress distribution and displacement on the middle maxilla point. In addition, the facemask with a miniplate anchorage showed a larger stress distribution area and sutural stress values than did the facemask with a tooth-borne anchorage. The pterygopalatine and zygomatico-maxillary sutures showed the largest sutural stress values with a facemask with a miniplate anchorage and after alveolar bone grafting, respectively.In this three-dimensional finite element analysis, it would be more advantageous to perform maxillary protraction using a facemask with a miniplate anchorage than a facemask with a tooth-borne anchorage and after alveolar bone graft rather than before alveolar bone graft, regardless of cleft type.