The atrioventricular node (AVN) has mystified generations of investigators over the last century and continues today to be at the epicenter of debates among anatomists, experimentalists, and electrophysiologists. Over the years, discrepancies have remained in regard to correlating components of AVN structure to function, as evidenced by studies from microelectrodes, optical mapping, and the electrophysiology laboratory. Historically, the AVN has been defined by classical histological methods; however, with recent advances in molecular biology techniques, a more precise characterization of structure is becoming attainable. Distinct molecular compartments are becoming apparent based on connexin staining and genotyping, providing new insight into previously characterized functional aspects of the AVN and its surrounding structures. Advances in optical mapping have provided a unique opportunity for correlating structure and function--unmasking properties of the native AVN pacemaker and providing further insight into basic mechanisms involved in AV conduction. Additionally, procurement of explanted human hearts have provided a unique opportunity to further characterize the human AVN structurally and functionally with both molecular biology techniques and optical mapping. With the elucidation of basic elements of both structure and function via molecular investigation and optical mapping, new opportunities are becoming apparent in utilizing the unique properties of the AVN for pursuing novel clinical applications relevant to clinical electrophysiology.