A newly developed software module for computer-assisted surgery based on a commercially available navigation system allows simultaneous, independent registration of two fragments and real-time navigation of both fragments while reduction occurs. To evaluate the accuracy three fracture models were used: geometric foam blocks, a pelvic ring injury with disruption of the symphysis and the sacroiliac joint, and a pelvic ring fracture with symphysis disruption and a transforaminal sacral fracture. One examiner did visual and navigated reduction and in all experiments the end point was defined as anatomic reduction. Residual displacement was measured with a magnetic motion tracking device. The results revealed a significantly increased residual displacement with navigated reduction compared with visual control. The differences were low, averaging 1 mm for residual translation and 0.7 degrees for the residual rotation, respectively. Residual displacement was small in both set-ups and may not be clinically relevant. Additional development of the software prototype with integration of surface registration may lead to improved handling and facilitated multifragment tracking. Use in the clinical setting should be possible within a short time.