An automated evoked potential analysis apparatus for monitoring, detecting and identifying changes to a patient's physiological system, wherein the apparatus comprises: an input device for obtaining electrical potential data from the patient's physiological system after application of stimulation to a patient's nerve; a computing system for receiving and analyzing the electrical potential data, and comprising 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 by calculating an ensemble average waveform of a first subset of the plurality of EPs, displaying the EA, calculating a second EA of a second subset of the plurality of EPs, wherein the second subset eliminates at least one initial EP from the first subset of EPs and includes at least one additional EP from after the termination of the first subset, and wherein the first and second subsets comprise the same number of EPs and represent a sliding window for generating a plurality of EAs; displaying on a display the second EA to display incremental changes in waveforms between the first and second subsets of EPs; and determine an alert vote for each subset of EPs, representative of changes to the physiological system generating the EPs wherein a positive alert vote is created if the acquired EP waveforms in a subset of EPs reach a change threshold in latency, amplitude or morphology compared with a previous subset of EPs; and trigger an alert when a ratio of positive to negative alert votes for a determined number of EAs exceeds a threshold value. an input device for obtaining electrical potential data from the patient's physiological system after application of stimulation to a patient's nerve; a computing system for receiving and analyzing the electrical potential data, and comprising 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 by calculating an ensemble average waveform of a first subset of the plurality of EPs, displaying the EA, calculating a second EA of a second subset of the plurality of EPs, wherein the second subset eliminates at least one initial EP from the first subset of EPs and includes at least one additional EP from after the termination of the first subset, and wherein the first and second subsets comprise the same number of EPs and represent a sliding window for generating a plurality of EAs; displaying on a display the second EA to display incremental changes in waveforms between the first and second subsets of EPs; and determine an alert vote for each subset of EPs, representative of changes to the physiological system generating the EPs wherein a positive alert vote is created if the acquired EP waveforms in a subset of EPs reach a change threshold in latency, amplitude or morphology compared with a previous subset of EPs; and trigger an alert when a ratio of positive to negative alert votes for a determined number of EAs exceeds a threshold value. 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 by calculating an ensemble average waveform of a first subset of the plurality of EPs, displaying the EA, calculating a second EA of a second subset of the plurality of EPs, wherein the second subset eliminates at least one initial EP from the first subset of EPs and includes at least one additional EP from after the termination of the first subset, and wherein the first and second subsets comprise the same number of EPs and represent a sliding window for generating a plurality of EAs; displaying on a display the second EA to display incremental changes in waveforms between the first and second subsets of EPs; and determine an alert vote for each subset of EPs, representative of changes to the physiological system generating the EPs wherein a positive alert vote is created if the acquired EP waveforms in a subset of EPs reach a change threshold in latency, amplitude or morphology compared with a previous subset of EPs; and trigger an alert when a ratio of positive to negative alert votes for a determined number of EAs exceeds a threshold value.