Systems and method for assessing a patients myocardial electrical stability by pacing a patients heart using a pacing sequence that includes at least two different types of pacing pulses. The pacing rate used is preferably only slightly above the patients intrinsic heart rate. A degree of alternans, in a signal (e.g., IEGM or ECG) that is indicative of cardiac activity in response to the pacing sequence, is determined. The degree of alternans can be determined by comparing portions of the signal that are indicative of cardiac activity in response to the first type of pacing pulses to portions of the signal that are indicative of cardiac activity in response to the second type of pacing pulses. The patients myocardial electrical stability is assessed based on the determined degree of alternans.
