An automated apparatus for real-time monitoring, detecting and identifying changes to a physiological system occurring during an ongoing clinical procedure, wherein the apparatus is configured to: provide electrical pulses to repeatedly stimulate peripheral nerves of the physiological system of a patient; acquire, over the course of an ongoing clinical procedure, resultant time sequence of responses or evoked potential waveforms generated by the physiological system through electrodes placed on the head or neck area of the patient; characterize and classify the recorded evoked potential waveforms by performing the steps of: (a) if a baseline response does not exist, estimating a baseline response and an analysis range based on acquired responses; (b) if the baseline response exists, updating the baseline response based on the current response; (c) characterizing the current response relative to the current baseline and the previous response in the sequence, and (d) classifying the current response as Good, Bad, Undetermined or Unreliable based on the characterization, wherein a Good classification indicates that the characterization corresponds with no significant waveform change, a Bad classification indicates that the characterization corresponds with a significant waveform change, an Undetermined classification indicates that the characterization is of indeterminate significance and the Unreliable classification indicates that the EP includes too much noise to be properly characterized and classified; wherein each classification corresponds to a threshold based on calculating at least one of a Euclidean distance, a pseudo-correlation, a cross-correlation, or an energy ratio between the resultant EP waveforms and the baseline EP; determine whether a current state of the peripheral nerves of the physiological system has changed from a Good state to a Bad state or vice versa based on the classification of the recorded EP waveforms by determining whether a count of resultant EP waveforms classified in a classification other than the current state exceeds a counter threshold; and provide an alert during the clinical procedure if the current state of the peripheral nerves has changed. provide electrical pulses to repeatedly stimulate peripheral nerves of the physiological system of a patient; acquire, over the course of an ongoing clinical procedure, resultant time sequence of responses or evoked potential waveforms generated by the physiological system through electrodes placed on the head or neck area of the patient; characterize and classify the recorded evoked potential waveforms by performing the steps of: (a) if a baseline response does not exist, estimating a baseline response and an analysis range based on acquired responses; (b) if the baseline response exists, updating the baseline response based on the current response; (c) characterizing the current response relative to the current baseline and the previous response in the sequence, and (d) classifying the current response as Good, Bad, Undetermined or Unreliable based on the characterization, wherein a Good classification indicates that the characterization corresponds with no significant waveform change, a Bad classification indicates that the characterization corresponds with a significant waveform change, an Undetermined classification indicates that the characterization is of indeterminate significance and the Unreliable classification indicates that the EP includes too much noise to be properly characterized and classified; (a) if a baseline response does not exist, estimating a baseline response and an analysis range based on acquired responses; (b) if the baseline response exists, updating the baseline response based on the current response; (c) characterizing the current response relative to the current baseline and the previous response in the sequence, and (d) classifying the current response as Good, Bad, Undetermined or Unreliable based on the characterization, wherein a Good classification indicates that the characterization corresponds with no significant waveform change, a Bad classification indicates that the characterization corresponds with a significant waveform change, an Undetermined classification indicates that the characterization is of indeterminate significance and the Unreliable classification indicates that the EP includes too much noise to be properly characterized and classified; wherein each classification corresponds to a threshold based on calculating at least one of a Euclidean distance, a pseudo-correlation, a cross-correlation, or an energy ratio between the resultant EP waveforms and the baseline EP; determine whether a current state of the peripheral nerves of the physiological system has changed from a Good state to a Bad state or vice versa based on the classification of the recorded EP waveforms by determining whether a count of resultant EP waveforms classified in a classification other than the current state exceeds a counter threshold; and provide an alert during the clinical procedure if the current state of the peripheral nerves has changed.