Third molar extraction is the most common procedure in oral and maxillofacial surgery. Third molars are considered less functional than other teeth and are often extracted. Sometimes, they are also used for auto-transplantation for the benefit of oral rehabilitation. Since many biological factors are involved in this surgical approach, herein, we outline a review of the biological characteristics of medico-legal/forensic interest, in addition to presenting a successful clinical case. A scoping review of currently available research data (following the principles of PRISMA-ScR or the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) on third molar auto-transplantation was conducted by drawing upon the main databases (Scopus, PubMed, Google Scholar and LILACS) to evaluate biological and clinical characteristics possibly relatable to forensic issues. All the collected data were summarized and elaborated on for the purpose of this article. A patient underwent extraction of the right upper first molar and auto-transplantation of the unerupted ipsilateral third molar. Many biologic and clinical factors are involved in the success of this clinical procedure. Knowledge of third molar anatomy, of its development and viable surgical approaches are all essential elements; just as important are the treatment of the tooth before and after transplantation and the integrity of the periodontal ligament. Follow-up of the clinical case for 5 years made it possible to verify the stability of the procedure over time. Third molar auto-transplantation is feasible and cost-effective. However, the use of third molars as donor teeth in auto-transplantation may have medico-legal implications. The lack of official protocols and consistent evidence-based guidelines for operators still prevent such a procedure from becoming mainstream; therefore, it is viewed with suspicion by clinicians and patients, even though the biological factors herein detected point to a reasonably high degree of safety. The understanding of many specific biological and clinical factors involved in the stability of third molar auto-transplantation allows for a thorough understanding of the forensic implications relevant to clinical practice. Effective communication and information provision are therefore of utmost importance, in the interest of both patients and doctors.