An automated evoked potential analysis apparatus for improved monitoring, detecting and identifying changes to a patient's physiological system is described. The apparatus includes an input device for obtaining electrical potential data from the patient's physiological system after application of stimulation to a patient's nerve and a computing system for receiving and analyzing the electrical potential data. The computing system includes a processing circuit configured to: generate a plurality of evoked potential waveforms (EPs) based on the electrical potential data, measure changes or trends in the generated EPs utilizing a sliding window of analysis, display incremental changes in waveforms between full subsets of EPs, and determine an alert vote for each subset, representative of changes to the physiological system generating the EPs.