Objectives: The detection of anatomical variation impairments in patients with cleft lip and palate (CLP) is crucial in combined orthodontic and maxillofacial surgical treatments. Therefore, this study aimed at evaluating the anatomical maxillary sinus characteristics, nasal septum deviation (NSD), and mucosal thickening of the maxillary sinus in patients with CLP using cone beam computed tomography (CBCT). Design: The CBCT images were classified into 3 groups of unilateral cleft lip and palate (UCLP; n = 40), bilateral cleft lip and palate (BCLP; n=14), and noncleft (control; n = 54). Subsequently, the maxillary sinus linear dimensions were assessed. Height, width, depth, infundibulum height, and ostium width were assessed as quantitative measures, whereas nasal septum deviation and mucosal thickening were assessed as qualitative measures. One-way analysis of variance and χ2 tests were utilized to identify any significant differences among the groups regarding the aforementioned variables. Results: Significant differences were observed among the groups regarding maxillary sinus height and depth, NSD, and mucosal thickening. Moreover, UCLP and BCLP groups showed higher incidence of NSD and mucosal thickening. However, the size of maxillary sinus height and depth was lower in the UCLP and BCLP groups. Conclusion: The results showed that BCLP and UCLP groups obtained lower maxillary sinus height and depth compared to the control group. On the other hand, incidence of the NSD and mucosal thickening was significantly higher in UCLP and BCLP groups than those in the control group.