A system and method are provided for obtaining registration of a localization systems three-dimensional coordinates for a plurality of markers having known locations to the two-dimensional coordinates for the plurality of reference markers obtained from a single X-ray image. The method for registering a navigational system with a localization system having a plurality of reference markers includes determining the three-dimensional coordinates of the locations of a plurality of reference markers within the localization coordinate system, and providing a single two-dimensional X-ray image that includes a two dimensional location of the plurality of markers. The method further includes determining a coordinate transformation for obtaining a best fit registration of the localization systems three-dimensional coordinates to the two-dimensional coordinates obtained from the single X-ray image, for at least one reference marker location.
