Maxillary sinus septa increase the risk of membrane perforation during sinus floor elevation and grafting operations. This study was designed to evaluate the prevalence, morphology, localisation, aetiology, and orientation of maxillary sinus septa in dentate, completely edentulous, and partially edentulous sinus regions using cone beam computed tomography (CBCT), and possible patient-related factors were also assessed. Data from 300 patients (600 sinuses), 160 women and 140 men, with a mean (SD) age of 50.72 (13.99) years (range 20–83), who were undergoing treatment planning for implant-supported restorations in posterior maxillae, were analysed from reformatted CBCT scans. Sinus septa were detected in 132 (44%) patients. A total of 208 septa were found, and 187 (31.17%) single maxillary sinuses presented septa in 600 sinuses. Unilateral septa were found in 77 patients (58.3%) and bilateral septa in 55 patients (41.7%). Out of the 208 septa, 42 (20.19%) were in the anterior third, 124 (59.62%) were in the middle third, and 42 (20.19%) were in the posterior third. Further, 106 (50.96%) septa were in completely edentulous regions, 64 (30.77%) were in partially edentulous regions, and 38 (18.27%) were in dentate regions. The prevalence of septa was significantly higher in the middle third area of the completely edentulous sinus regions. The mean (SD) height of septa was 6.34 (3.05) mm, and the mean orientation was buccopalatal in 204 patients (98.08%). Maxillary sinus septa are common anatomical structures. To avoid possible complications during sinus augmentation, a detailed radiographic identification of anatomical structures in maxillary sinuses is needed.