Structural or anatomic differences may arise during the development of the maxillary sinus and the process of fusion of the palate in the presence of cleft lip and palate. The present study aimed to compare the maxillary sinus volume of patients with unilateral cleft lip and palate and a control group (noncleft patients). In this retrospective case-control study, 160 cone-beam computed tomography images of 80 unilateral cleft lip and palate patients (41 males and 39 females; mean age, 12.7±6.03years) and 80 control patients (43 males and 37 females; mean age, 13.1±6.27years) were evaluated through the ITK-SNAP software (Cognitica, Philadelphia, Pa) to access the maxillary sinus volume. Analysis of covariance and regression analysis were used to assess the differences between the groups while considering the relationship between maxillary sinus volume, age, and sex. No statistically significant differences were found in the maxillary sinus volume analyzing a unilateral cleft lip and palate and a control group (P=0.677). Considering the cleft group, there is a tendency for the maxillary sinus volume of the cleft side to be smaller than its contralateral (P<0.001). Statistically significant differences were found in the maxillary sinus volume, regarding the age and sex of cleft and noncleft patients (P<0.001 for age; P=0.001 for sex). According to these results, the presence of unilateral cleft lip and palate did not affect the maxillary sinus volume, comparing cleft and noncleft patients. A biphasic growth pattern of the maxillary sinus and a presence of sexual dimorphism were found.