A technique is described for in vivo localization of microelectrodes during single-unit recording in the alert monkey. Four hollow glass spheres filled with copper sulfate and iohexol were affixed to the surface of the animal's skull prior to the acquisition of a series of coronal magnetic resonance (MR) images. These reference beads were visible in both X-ray and MR images. Cranial recording chambers were then implanted bilaterally over the amygdaloid complex. A microelectrode was advanced to various depths in the subject's brain. At each selected microelectrode site, five radiographs were obtained and a small electrolytic lesion was made. Based on the data from the radiographs, we computed the position of the microelectrode tip at each site relative to the reference beads. With a precision of 625 microns, this method was used to predict the neuroanatomical location of ten microlesions placed in both subcortical and cortical structures. Postmortem histological analysis revealed that the actual location of the lesions closely matched predictions arrived at using the X-ray/MRI localization technique. This technique thus provides an accurate, reliable and noninvasive method for in vivo localization of microelectrode recording sites.