A three-dimensional anatomically and electro-physiologically realistic model of atrial propagation is developed utilizing generic cardiac ionic models fitted to experimentally recorded action potentials (APs). The atrial geometry incorporated realistic wall thickness and twelve anatomical structures, including the sino-atrial node (SAN), pulmonary veins, interatrial septum, Bachmann's bundle and coronary sinus as interatrial conduction pathways. The SAN was further subdivided into central and peripheral regions, characterized by different ionic parameters. These parameters were obtained by optimizing ionic models to fit spontaneous APs recorded intracellularly from intact rabbit in vitro sino-atrial tissue preparations. The SAN region in the 3D model was able to initiate spontaneous rhythmic APs and excite the surrounding atrium. The pattern of atrial activation was similar to that observed in humans. The use of model optimization allows direct incorporation of experimental data into anatomically realistic geometries and is a step towards developing patient-specific models for the treatment of atrial arrhythmias.