The removal of wisdom teeth is one of the most common interventions in oral surgery. In order to avoid complications, a profound knowledge of the anatomy of teeth and adjacent tissues is crucial. In the case of maxillary wisdom teeth, their relationship to the maxillary sinus, to the pterygoid fossa, to the maxillary tuber and the adjacent venous plexus is particularly important. Three-dimensional (3D) imaging, for example by means of cone beam computed tomography (CBCT), is increasingly utilized in practice. However, the necessity of CBCT imaging is still a matter of intensive debate. The aim of this study was to describe the anatomic (positional) variation of maxillary wisdom teeth and, based on these findings, to elucidate the additional benefit of such imaging. A retrospective case study was performed using patients examined by means of CBCT imaging in the Department of Dento-Maxillofacial Radiology during the period from 2008 to 2013. Primary study variables comprised the spatial relationship of the teeth to the maxillary sinus, the degree of retention and root development, the covering of the root with bone and mucosa, the root configuration, and the developmental stage of the tooth. In addition, the association of the inclination of teeth in the transversal and sagittal plane with the above variables was evaluated. Descriptive statistical parameters were calculated for all results of the examination. In total, CBCT recordings of 713 maxillary wisdom teeth from 430 patients were evaluated. Their mean age was 29.8 years, and the proportion of male patients slightly prevailed (54.4%). Most teeth exhibited fully developed roots (64.1%). Overall 22.9% of third molars were impacted, 32.3% were retained, and 6.5% were erupting. In more than a third of the patients, wisdom teeth were in occlusion. The inclination of the third molars both in the transversal and sagittal plane was significantly associated with the distance of the root from the maxillary sinus as well as with the bony covering of the root. Owing to the possibility of evaluating preoperatively the relationship of a wisdom tooth to the maxillary sinus and to other anatomic structures, we recommend the use of CBCT, whenever conventional radiography fails to provide adequate information about the critical anatomic circumstances of maxillary third molars. However, CBCT should, at least nowadays, not be utilized as the standard radiographic examination.