The ultimate goal of endodontic microsurgery is the predictable regeneration of periapical tissues and osseous defects. Although every step of endodontic microsurgery has dramatically improved over the past years, little attention has been paid to the bone defect topography underlying the soft tissue. This paper presents a classification of bony defects as faced during endodontic microsurgery, discusses current techniques and materials for the management of such lesions and describes the clinical procedures for the management of bony defects. Keywords: endodontic microsurgery, guided bone regeneration, guided tissue regeneration, osteogenesis