Abstract: A computer-implemented method and system for guiding the placement of orthodontic brackets are provided. The system can include an at least one indexing tool designed to conform to at least a portion of a patient's teeth or alveolar process. The system can receive signals from a sensor at the indexing tool as well as signals from a sensor at a bracket positioning tool in order to track spatial location—and/or orientation of one or more brackets relative to the surface of the patient's actual or modeled teeth. A method for guiding the placement of orthodontic brackets involves detecting the location and/or orientation of a bracket with respect to at least one tooth of a patient and notifying the orthodontist that the actual bracket position and/or orientation meets specified criteria with respect to planned placement coordinates for the bracket. The method can further include collecting the planned placement coordinates for each bracket tooth combo during a planning phase.