Aim of this investigation is to evaluate prevalence, localization, and height of 114 maxillary sinus septa by using cone-beam computed tomography scans. The thickness of the mucosa has been measured together with the variations of the membrane in relation to those septa. A total of 228 maxillary sinuses have been considered. Septa were identified using "panorex" reconstructions and axial scans of cone-beam computed tomography using the software "eXamVision." The thickness of the mucosa has been evaluated in the paraxial scans and related to those septa where they were present. In the current study, the prevalence of sinus septa is 38.1%. Significant difference can be found in the height of primary and secondary septa. The mean height of primary septa was 5.5 mm (± 1.19) and of secondary septa 3.4 mm (± 1.6). Anterior and medium septa resulted significantly higher than posterior septa (P = 0.003). The medium thickness of the mucosa was 0.85 mm (± 0.58), whereas close to the septa it turned out to be 1.8 mm (± 1.87). The difference is statistically relevant (P = 0.003). There is no statistically significant proportional relation between dimensions of septa and thickness of mucosa (P = 0.53). Underwood septa are frequent anatomic variations of the maxillary sinus. Their presence may result in a thickening of the sinus membrane. The systematic study of radiographic anatomy of maxillary sinus is necessary before the sinus lift surgery planning.