To evaluate the anatomy and variations of osteomeatal complex (OMC) by comparing patients with nonsyndromic cleft lip and palate (CLP) and control group. This case-control study was retrospectively analyzed using cone-beam computed tomography data. Istanbul University Faculty of Dentistry Department of Dentomaxillofacial Radiology. The study was conducted with 100 patients (44 females, 56 males) with CLP and 100 patients in the control group, which matched gender and age (with a maximum difference of 3 years). OMC variations are grouped as follows: ethmoidal, conchal, uncinate process, and septal variations. Then, we evaluated the presence of these OMC variations and compared them between the two groups. The McNemar's test was used to determine any significant differences between the groups for all indices at the 95% confidence level. The most common anatomic variation in this study was Agger nasi cell (97%) and concha bullosa (97%) in the patients with CLP, while Agger nasi cell was the most common variation (99%) in the controls. Moreover, the atelectatic uncinate process was the least observed variation in both groups (1%). The incidences of paradoxical concha (58%;42%), bifid concha (29%;11%), deviated nasal septum (92%;80%) were significantly higher in the CLP group (p < 0.05). The statistically significant results found when comparing OMC anatomy between the two groups reveal the importance of three-dimensional evaluation before functional endoscopic sinus surgery in patients with CLP.