Apical endodontic surgery is applied frequently following a failed conventional endodontic treatment. The apical preparation can be carried out conventionally using a round bur or using an endodontic ultrasonic system. The purpose of this study was to compare the outcome of the 2 treatment options by a randomized prospective clinical study. Patients (n=399) were at random allocated to treatment using a conventional round bur or using an ultrasonic system (P-max Newtron) according to a for the rest similar treatment protocol. One year post treatment, the treatment outcomes were determined by 2 oral and maxillofacial surgeons, blinded for the treatment option. Adequate follow-up data were obtained from 290 patients. The overall success rate was 71% in the patients treated conventionally and 81% in the patients treated using the ultrasonic system. In molar teeth, the difference in success rate was statistically significant.