Recent work has demonstrated the accuracy and operational viability of an algorithm proposed by the authors that successfully registers 3-D ultrasound data with CT or MRI data. The successful application of this method to intraoperative navigation, however, depends critically on the quality of the acquired ultrasound data. This gives rise to two questions concerning the usability of the algorithm in clinical praxis. First, how can one guarantee high-quality, user-independent ultrasound registration data with this procedure? Second, can this approach work reliably in clinical practice, namely within the operating theater? To address both of these questions, we present an ultrasound data acquisition protocol that leads the user through the data acquisition process and also provides the criteria to adjust the relevant ultrasound parameters. We also evaluated criteria for the visual inspection of the suitability of the ultrasound data for the registration process. Results for this evaluation show that these visual criteria can be used to decide preoperatively if an ultrasound registration will be successful in a patient. The intraoperative evaluation of the protocol showed that high-quality registrations can be achieved under realistic conditions. This protocol and the visual inspection criteria, together with the ultrasound registration algorithm, provide a surgical team with a means of performing precise, cost-effective navigation in patients for whom a navigated intervention was previously impossible. We evaluated the proposed procedure in clinical practice.