Surgical removal of impacted third molars is one of the most frequent procedures in oral surgery. Here, three-dimensional (3D) imaging is often used, yet its necessity is still being heavily debated. The aim of the study was to describe the variation in the anatomical positioning of third mandibular molars, and, by doing so, examine the necessity of 3D imaging. A retrospective case study was performed with the patients from an oral surgery department from January 2009 to February 2013. The primary focus of the study was on the spatial relationship to the mandibular canal, as well as angulation, root configuration, and developmental stage of the wisdom tooth. Descriptive statistics were calculated for these variables. A total of 1197 wisdom teeth in 699 patients were evaluated. 46.7% exhibited direct contact to the mandibular canal, another 28.7% showed close proximity and 24.6% a measurable distance. In 29.0%, the mandibular canal was vestibular and in 23.8% lingual to the wisdom tooth. In 7.4%, it was interradicular and in 0.6% intraradicular. Most teeth had one (21.3%) or two (55.3%) roots. Others had three (17.6%), four (2.0%) or five (0.2%) roots. In 31.4% of the teeth, the root perforated the lingual compact bone, and in 4.3% the vestibular compact bone. 44.4% of the teeth had mesial angulation, 9.7% distal angulation, 35.3% lingual and 2.9% buccal angulation. Due to the anatomical variety, the use of 3D imaging is recommended before surgical removal of mandibular third molars if conventional imaging cannot exclude complicated conditions.