Objective The purpose of this study is to evaluate the sphenoid sinus variations in patients with cleft lip/palate. Methods Sixty three (63) patient's cone beam computed tomography (CBCT) images, taken from the head and neck region, were evaluated. Images were divided into two groups; [Group 1; patients with cleft lip/palate (CLP Group) (n = 23) Group 2; patients without cleft lip/palate (control group) (n = 40)]. The main pneumatization types (conchal, sellar, and presellar) of sphenoid sinuses were assessed on sagittal sections of the CBCT images. The sphenoid body, lateral and lesserwing types were evaluated on coronal sections and anterior type pneumatization was evaluated on axial sections. Results The mean age ranged from 12 to 26 (16.57 +/- 4.46) in Group 1 and 12 to 25 (16.58 +/- 3.71) in Group 2. In both groups, the male and female distribution was found similar (P = 0.342). The sellar type was the most common pneumatization type of sphenoid sinus both for the Group 1 (91.3%) and Group 2 (80%). Any statistically significant difference was not found between the two groups in terms of the incidence of pneumatization types. Combined type pneumatization was detected in 65.6% of the Control group and 76.2% of the CLP group. Conclusions In this study, the prevalence of sphenoid sinus pneumatization types in CLP patients was compared with the normal population. Any significant difference was not determined in the two groups.