Background and Objectives: Anatomical variations in the head, neck and chest are common, and are observed as occasional findings on computed tomography (CT). Although anatomical variations are mostly asymptomatic and do not cause any negative influence on the body function, they may jeopardize diagnosis and may be confused with pathological conditions. The presence of variations may also limit surgical access during tumor removal. The aim of this study was to investigate the prevalence of six anatomical variations—os acromiale, episternal ossicles, cervical rib, Stafne bone cavity, azygos lobe and tracheal bronchus—in an open-access computed tomography dataset obtained from oropharyngeal cancer patients. Materials and Methods: A total of 606 upper-chest and neck computed-tomography scans (79.4% male and 20.6% female) were retrospectively investigated. Sex difference was evaluated using the z-test for two proportions. Results: Os acromiale, episternal ossicles, cervical rib, Stafne bone cavity, azygos lobe, and tracheal bronchus were present in 3.1%, 2.2%, 0.2%, 0%, 0.3% and 0.5%, respectively, of all patients. Os acromiale was identified as meso-acromion in 86.6%, and as pre-acromion in 17.4%, of all acromia. Episternal ossicles were present unilaterally in 58.3%, and bilaterally in 41.7%, of all sterna. Only the cervical rib showed a sex difference in prevalence. Conclusions: awareness of these variations is important for radiologists interpreting head, neck and chest CTs; for example, those of oropharyngeal cancer patients. This study also illustrates the applicability of publicly available datasets in prevalence-based anatomical research. While most of the variations investigated in the present study are well-known, the episternal ossicles are not well explored, and need further investigation.