Auditory Brainstem Responses (ABRs) are a reliably robust measure of auditory thresholds in the mammalian hearing system and can be used to determine deficits in the auditory periphery. However, because these measures are limited to the lower stages of the auditory pathway, they are insensitive to changes or deficits that occur in the thalamic and cortical regions. Cortical Auditory Evoked Potentials (CAEPs), as longer latency responses, capture information from these regions. However they are less frequently used as a diagnostic tool, particularly in rodent models, due to their inherent variability and subsequent difficult interpretation. The purpose of this study was to develop a consistent measure of subcutaneous CAEPs to auditory stimuli in mice and to determine their origin. To this end, we investigated the effect on the CAEPs recorded in response to different stimuli (noise, click, and tone (16 kHz) bursts), stimulus presentation rates (2/s, 6/s, 10/s) and electrode placements. Recordings were examined for robust CAEP components to determine the optimal experimental paradigm. We argue that CAEPs can measure robust and replicable cortical responses. Furthermore, by deactivating the auditory cortex with lidocaine we demonstrated that the contralateral cortex is the main contributor to the CAEP. Thus CAEP measurements could prove to be of value diagnostically in future for deficits in higher auditory areas