The system and method discriminates P-waves or other electrical events originating in the atria from R-waves or other electrical events originating in the ventricles. In one example, far-field R-waves in the atria are distinguished from true P-waves using both a post-ventricular atrial blanking (PVAB) interval and a separate pre-ventricular blanking interval (pre-VAB) interval. Insofar as the pre-VAB interval is concerned, upon detection of a P-wave in the atria, the implantable medical device begins tracking a pre-VAB interval. If an R-wave is then detected in the ventricles during the pre-VAB interval, the P-wave is rejected as being a far-field R-wave. A PVAB interval may also be employed to filter out any P-waves detected in the atria immediately following detection of an R-wave in the ventricles. In another example, far-field R-waves are distinguished from true P-waves using template matching. P-waves detected in the atria are compared against a template representative of true P-waves. If the P-wave substantially matches the template, the P-wave is deemed to be a true P-wave; otherwise, the P-wave is rejected as being a far-field R-wave or other anomalous electrical event. In both examples, the techniques are applicable to other types of electrical events detected within the heart besides P-waves and R-waves, such as electrical events occurring during fibrillation or flutter when discrete P-waves and R-waves may not be detectable.