The invention relates to a method and device for performing coordinate transformation for navigation-guided procedures using an imaging diagnostic tool, especially an X-ray diagnostic tool, and a position-determining system. In the vicinity of the image receiver, the diagnostic tool has one or more three-dimensional reference structure that can be touched with a pointer of a position-determining system. From the known geometry of the three-dimensional reference structure and the coordinates of the touched points determined by the position-determining system, a coordinate transformation is created between the coordinate system of the diagnostic tool and the coordinate system of the position-determining system. Navigation for an instrument captured by the position-determining system can be performed in reconstructed images of the diagnostic tool after the registration procedure.