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One of the major challenges in electromagnetic navigated bronchoscopy is the navigation accuracy. An initial rigid image-to-patient registration may not be optimal for the entire lung volume, as the lung tissue anatomy is likely to have shifted since the time of computer tomography (CT) acquisition. The accuracy of the initial rigid registration will also be affected throughout the procedure by breathing, coughing, patient movement and tissue displacements due to pressure from bronchoscopy tools. A method to minimize the negative impact from these factors by updating the registration locally during the procedure is needed and suggested in this paper.The intraoperative local registration method updates the initial registration by optimization in an area of special interest, for example, close to a biopsy position. The local registration was developed through an adaptation of a previously published registration method used for the initial registration of CT to the patient anatomy. The method was tested in an experimental breathing phantom setup, where respiratory movements were induced by a robotic arm. Deformations were also applied to the phantom to see if the local registration could compensate for these.The local registration was successfully applied in all 15 repetitions, five in each of the three parts of the airway phantom. The mean registration accuracy was improved from 11.8–19.4 mm to 4.0–6.7 mm, varying to some degree in the different segments of the airway model.A local registration method, to update and improve the initial image-to patient registration during navigated bronchoscopy, was developed. The method was successfully tested in a breathing phantom setup. Further development is needed to make the method more automatic. It must also be verified in human studies.