The use of stereotaxic neurosurgery in rodent models of human disease requires the alignment of central nervous system (CNS) structures that can be identified and surgically approached with great accuracy. Current technologies make possible development of mouse lines with enhanced predispositions for the development of various diseases including tumors. When such tumors arise in the brain their location is unpredictable. Obtaining a biopsy or stereotaxically delivering local therapy requires that the site of such tumors be known with great precision. We devised a method to correlate images of mouse brain tumors acquired by magnetic resonance imaging (MRI) with stereotaxic coordinates that can be used for obtaining biopsies or administering local therapy. We constructed a head holder containing a pair of tubes filled with a substance that could be imaged by MR and which were separated by varying distances. This allowed the precise localization of the tumor in all three dimensions. The strategy we employed is adaptable to other imaging modalities and to other body sites.