A multi-electrode system that permits simultaneous recordings from multiple neurons and iontophoretic applications at two or three different brain sites during acute experiments is described. This system consists of two or three microdrive terminals, each of which includes four electrodes that can be moved independently and used for both extracellular recordings and microiontophoretic drug administration. Drug applications were performed during standard extracellular recordings of multiple single-units via specialized combined electrodes (CEs), which enable ejection of neuroactive substances and recording of neuronal activity from the same electrode. With this system, we were able to successfully record simultaneously from different levels (brainstem, thalamus, and cortex) of the vibrissal ascending pathway of the anesthetized rat. Herein, examples of simultaneous recordings from the brainstem and thalamus and from the thalamus and cortex are presented. An effect of iontophoretic applications of agonists and antagonists of metabotropic glutamate receptors (mGluRs) in the thalamus is demonstrated, and the extent of drug diffusion in the barrel cortex is demonstrated with biocytin. This new multi-electrode system will facilitate the study of transformations of sensory information acquired by the whiskers into cortical representations.