Background: A separated instrument complicated orthograde endodontic retreatment of a maxillary molar tooth with apical periodontitis. Methods: The tooth was treated utilizing microsurgical techniques that employed an operating microscope, ultrasonics, micro-instrumentation and mineral trioxide aggregate as a root-end filling material. Results: Healing was evident at a 12-month review appointment. Conclusions: Microsurgical techniques have significantly improved the outcomes for healing of periapical lesions when compared to traditional approaches to endodontic surgery. Success rates have been shown to be comparable with conventional orthograde treatment.