Background: Heart rate variability (HRV) measurements are usually performed from ventricular beat- to-beat intervals because of the difficulty to precisely locate the P-wave fiducial point in surface ECG recordings. Intracardiac electrogram can be recorded by pacemaker device. This provides useful signals to measure atrial and ventricular heart rate variability.Objective: to describe a method which measure the atrial and ventricular heart rate variability using intracardiac electrogram recorded and stored by pacemaker devices.Method: The study was conducted on 14 patients with dual chamber pacemakers. Those were suffering from intermittent sick sinus diseases or intermittent advanced A-V block attending the Cardiac Care Unit in Al-Kadhimiya Teaching Hospital. The atrial and ventricular intracardiac electrograms were transmitted with the telemetry channel of the pacemaker to an external recorder for 20 minutes. The resultant intervals were used to calculate the standard deviation of all N-N intervals (SDNN), the squared root of the mean squared differences of successive N-N intervals (RMSSD), and the percentage of successive interval differences> 50 ms (pNN50). The differences between atrial and ventricular heart rate variability indexes (HRVIndexes)were assessed for each patient with a cut-off point of 1%. Differences >1% were analyzed in detail.Results: Fourteen patients with dual chamber pacemakers were included in this study. A total of 18788 heart cycles were analyzed. A manual correction due to false or not triggered atrial or ventricular events was necessary in 0.8%. The overall differences between atrial and ventricular pNN50 was -0.5%±2.1% and differences > 1% were observed in 4 patients. The N-N50 events occurred in the atrial and related ventricular interval in 84%. N-N50 events occurred only the atrium in 6% and only I the ventricle in 10%. The mean differences between atrial and ventricular SDNN and RMSSD were 0.4±2.1 ms and -0.1±3.5 ms with individual differences <1%.Conclusion: This study describes the utilization of intracardiac electrograms to analyze differences between atrial and ventricular HRV. The differences for pNN50 indicate that ventricular HRV does not reflect the changes of sinus node activity in all patients.