A method of identifying the fossa ovalis in a patient by positioning one or more electrodes against the tissue of the interatrial septum of the patient and acquiring unipolar and/or bipolar electrograms of the tissue of the interatrial septum while moving the electrodes to a plurality of positions against the tissue of the interatrial septum. The fossa ovalis is identified on the basis of unipolar voltage reduction, signal fractionation, broadened signal, reduced signal slew rate, reduced local myocardial impedance, increased phase angle and/or increased pacing threshold. An apparatus for identify the fossa ovalis is also provided.