Laparoscopic surgery is performed through small incisions that limit free sight and possibility to palpate organs. Although endoscopes provide an overview of organs inside the body, information beyond the surface of the organs is missing. Ultrasound can provide real-time essential information of inside organs, which is valuable for increased safety and accuracy in guidance of procedures. We have tested the use of 2D and 3D ultrasound combined with 3D CT data in a prototype navigation system. In our laboratory, micro-positioning sensors were integrated into a flexible intraoperative ultrasound probe, making it possible to measure the position and orientation of the real-time 2D ultrasound image as well as to perform freehand 3D ultrasound acquisitions. Furthermore, we also present a setup with the probe optically tracked from the shaft with the flexible part locked in one position. We evaluated the accuracy of the 3D laparoscopic ultrasound solution and obtained average values ranging from 1.6% to 3.6% volume deviation from the phantom specifications. Furthermore, we investigated the use of an electromagnetic tracking in the operating room. The results showed that the operating room setup disturbs the electromagnetic tracking signal by increasing the root mean square (RMS) distance error from 0.3 mm to 2.3 mm in the center of the measurement volume, but the surgical instruments and the ultrasound probe added no further inaccuracies. Tracked surgical tools, such as endoscopes, pointers, and probes, allowed surgeons to interactively control the display of both registered preoperative medical images, as well as intraoperatively acquired 3D ultrasound data, and have potential to increase the safety of guidance of surgical procedures.