A system and method for estimating optimal atrioventricular delay values for use in pacing the ventricles. Both the intrinsic inter-atrial conduction delay and the intrinsic atrioventricular conduction delay are determined for the patient and then the preferred atrioventricular pacing delay is derived therefrom. By taking into account intrinsic inter-atrial delay along with intrinsic atrioventricular delay, a more reliable estimate of the true optimal atrioventricular delay values for the patient can be achieved than with techniques that only take into account intrinsic atrioventricular delay values. In one example, the technique uses intracardiac electrogram (IEGM) signals and surface electrocardiogram (EKG) signals and hence can be performed by an external programmer without requiring Doppler echocardiography or other cardiac performance monitoring techniques. In another example, wherein the implanted device is equipped with a coronary sinus lead, the technique uses only IEGM signals and hence can be performed by the device itself.