A method and system for initializing a pacemaker includes receiving electrophysiology (EP) data from an intra-body EP catheter or catheters positioned relative to a patient's heart, calculating a patient specific pacemaker operating parameter or parameters from the received EP data and programming the pacemaker to operate based on the calculated patient specific pacemaker operating parameter or parameters. Stimulation of the patient's heart using the EP catheter or catheters based on the calculated pacemaker operating parameter or parameters may then be accomplished to determine whether the patient's heart achieves an acceptable physiological response when stimulated based on the calculated pacemaker operating parameter or parameters, and recalculation of the pacemaker operating parameter or parameters may be accomplished if the stimulation fails to achieve the acceptable physiological response.