Objective: Cleft lip and/or palate (CLP) is one of the most common congenital craniofacial anomalies. Individuals with CLP experience numerous problems including lack of nutrition, impaired speech, hearing loss, obstruction of nasolacrimal duct, poor dentition and facial morphology, and sinusitis. This study aimed to compare the nasolacrimal canal morphometry (nasolacrimal duct [NLD]), maxillary sinus ostium (MSO) localization, and presence of the accessory maxillary ostium (AMO) in patients with unilateral or bilateral CLP with healthy controls. Materials and Methods: The transversal and anteroposterior diameters and the length of the NLD were measured in 33 patients with unilateral CLP and 30 patients with bilateral CLP using cone-beam computed tomography. There were 16 (53.3%) males and 14 females (46.7%) in the bilateral CLP group and 18 males and 15 females in the unilateral CLP group. The mean ages of the patients were 17.36 ± 5.27 in patients with unilateral CLP and 18.6 ± 5.66 in patients with bilateral CLP. The anteroposterior location of the MSO and AMO was evaluated. Results: The transversal (P = 0.003) and anteroposterior (P = 0.002) diameters of NLD were found to be significantly different between the patients with bilateral CLP and the control group. The NLD length was found to be significantly different between the control group and the affected sides in the unilateral CLP group (P = 0.02). The MSO was found more in the middle region in the control group compared to the unilateral CLP group (P = 0.004). The AMO was found in 66.7% of the patients with bilateral CLP and 62.1% of the patients with unilateral CLP. The AMO was found more in the control group than in the bilateral CLP group (P = 0.01). Conclusions: Cleft lip and palate is an anomaly that can affect both the diameter and the length of the NLD and MSO localization.