An implantable monitoring device is disclosed for monitoring a patient's heart rate variability over time. The device includes a cardiac electrogram amplifier, a sensing electrode coupled to an input of the amplifier, timing circuitry, processing circuitry and a memory. The timing circuitry defines successive shorter time periods during each monitoring period. The processing circuitry relies upon electrogram activity that occurs during rest periods that extend as long as T1, all of which is stored into memory. Active periods are not considered as part of the heart rate variability calculation. The processing circuitry calculates median intervals between depolarizations of the patient's heart sensed by the amplifier during the shorter time periods and calculates a standard deviation of the median intervals during T2, a longer monitoring period.
