Abstract Background Maxillary sinus septa increase perforation risk of Schneiderian membrane during the sinus floor elevation (SFE). Cone Beam Computed Tomography (CBCT) allows for a more precise assessment of the septal position; thus, preoperative CBCT analysis is substantial to avoid possible complications. This study aims to investigate the 3D characteristics of the maxillary sinus septa based on CBCT images. To our knowledge, no study reported the CBCT-based investigation for the sinus septa among Yemeni population. Materials and methods This is a retrospective cross-sectional analysis of 880 sinus CBCT images 440 patients. The septa prevalence, locations, orientations, morphology, and associated factors were analyzed. The effect of age, gender, and dental status on the sinus septa and the relationship between sinus membrane pathology and sinus septa were also analyzed. Anatomage (Invivo version 6) was used for CBCT images analysis. Descriptive and analytical statistics were performed, and a P-value