The development of the maxillary sinus is different in patients with cleft lip and palate (CLP) compared to non-CLP individuals. To investigate the prevalence and features of maxillary sinus septa (MSS) in patients with CLP in comparison with the non-CLP population. Retrospective study. Cone beam computed tomography (CBCT) evaluation. CLP center in Shiraz faculty of dentistry, Iran. A total 306 sinuses (88 cleft and 218 noncleft) on 153 images (CLP group: n = 66; control group: n = 87) were examined to determine the prevalence of septa and characterize them. Sinus septa were characterized according to height, orientation, angle, origin, and location. The chi-square test, Mann-Whitney U test, and Fisher's exact test were used for statistical analysis. The prevalence of septa was 28.9% and 32.1% in the CLP and control groups, respectively. No significant difference was found between the study groups in terms of prevalence, location, and orientation of MSS. The average height and angle of septa were significantly higher in the control group compared to the CLP group. Inferior origin was significantly more prevalent in the control group than in the CLP group (P = .004). There was no difference in the prevalence of MSS between patients with CLP and non-CLP individuals. However, certain features of the septa were different in patients with CLP.