The foramen tympanicum, also known as the foramen of Huschke (FH), is a permanent anatomical variation situated in the anteroinferior section of the external auditory canal, posteromedial to the temporomandibular joint. The aim of the study is to determine the prevalence of the FH in Cleft Lip and Palate (CL/P) patients, compared to healthy individuals by using Cone Beam Computed Tomography (CBCT) data. We retrospectively analyzed the CBCT images of 272 individuals, who had been referred to our Oral and Maxillofacial Radiology clinic various reasons. For comparison, 226 randomly selected healthy individuals and 46 CL/P patients (35 unilateral and 11 bilateral) were evaluated. FH in 35 (12.9%) of the 272 individuals; 26 of them healthy individuals, 9 of them CL/P patients. The FH was higher in patients with CL/P (19.6%) than healthy individuals (11.5%). Clinicians should be aware of the variability of THE and especially the FH in the ear region when radiographically amining these sites prior to CL/P surgery to prevent postoperative reconstruction and complications. Moreover, to evaluate these anatomical variations, CBCT examinations can be used instead of CT scans.