We developed an experimental system to simultaneously characterize tonotopic activities of both the auditory cortex and thalamus of rats, each with a number of microelectrodes. The system consisted of a custom-designed surface electrode array and depth electrode array. The surface electrode array had 64 recording points in a 4.5 mm × 3 mm area. Between the recording points holes were made, through which the depth array was inserted. The depth array had 3 shanks, each of which was 6 mm long with an inter-shank distance of 500 µm. Each shank had 15 recording sites for the thalamus and 17 for the auditory cortex. To precisely insert the depth array perpendicularly to the cortical surface, a laser displacement meter was used. We measured tone-evoked local field potentials and multi-unit activities in the auditory cortex and thalamus of rats under anesthesia, and characterized tonotopic maps simultaneously in the auditory cortex and thalamus.