In bats conventional stereotaxic methods do not yield sufficient positional accuracy to allow reliable recordings and tracer injections in subnuclei of the auditory system. In a newly developed stereotaxic system experimentally measured patterns of skull profile lines are used to define the animal's brain position with an accuracy of +/- 100 microns. By combining the neurophysiological stereotaxic procedure with a standardization of the neuroanatomical processing of the brains, the location of recordings, stimulations or injections can be readily transformed into brain atlas coordinates. This facilitates the compilation and comparison of data within and among animals. The system is not restricted to use in bats and can be readily adapted to other experimental animals.