Surgical guides and three-dimensional (3D) planning softwares used in everyday dental implantology open new possibilities in other fields of dentistry. While using the operation microscope in endodontic microsurgery provides more precise apicectomy, there is still no consent on the exact localisation and size of the bony window to be prepared for this surgery. Our aim is to describe a new, guided endodontic microsurgery method when osteotomy and apicectomy are planned in a 3D software and performed with a trephine bur. Based on data from Cone Beam Computed Tomography, planning of the surgical guide was performed with a 3D planning software (Smart Guide, dicomLAB, Hungary) in order to define the size of the bony window, the angulation and the depth of the trephine bur during the apicectomy. After preparing a mucoperiosteal flap, with the help of the dentally supported surgical guide, the trephine bur removes the cortical bone and the apex of the root simultaniously. Following the modern microsurgical protocol, after performing the ultrasonic retrograde preparation, mineral trioxide aggregate (ProRoot MTA; Dentsply Maillefer, Ballaigues, Switzerland) is placed as a retrograde filling to close the resected area. After the uneventful healing period, a complete bony regeneration can be seen on the 1-year follow up X-ray. The patient is symptom-free. This technique is considered to be faster and more precise than the non-guided endodontic microsurgery carried out without the utilization of a trephine bur. Orv Hetil. 2020; 161(30): 1260-1265.