Introduction: Mini-implants are widely used for predictable tooth movements, but insertion is often restricted by anatomic structures. The aims of this study were to investigate the incidence of penetration of mini-implants into the sinus and the relationship between penetration depth and sinus tissue. Methods: Data from 32 patients who received mini-implants in the infrazygomatic crest were collected from a data base. The success rate of mini-implants was determined by clinical retrospective analysis. The incidence of penetration, penetration depth, and sinus configuration were investigated and compared between cone-beam computed tomography scans obtained immediately after insertion and before mini-implant removal. Results: The overall success rate of mini-implants in the infrazygomatic crest was 96.7%, and 78.3% penetrated into the sinus. In the group in which penetration exceeded 1 mm, the incidence of membrane thickening was 88.2%, and the mean value of thickening was 1.0 mm; however, the variable values of penetration in the 1-mm group were only 37.5% and 0.2 mm, respectively (P <0.05). The incidence of penetration of infrazygomatic crest mini- implants into the sinus may be high. Penetration through double cortical bone plates with limitation of the penetration depth within 1 mm is recommended for infrazygomatic crest mini-implant anchorage.