Introduction 3D computer models of the heart are important tools for teaching, research and drug discovery. In current human heart models, the heart’s wiring system (the cardiac conduction system, CCS) is oversimplified or omitted and the aim of this study is to create a 3D model including the CCS: the sinus node (SN), the paranodal area (transitional pacemaker tissue bordering the sinus node; PN (1)), atrioventricular node (AVN) and His-Purkinje system. Methods A whole human heart as well as an isolated human SN preparation (intercaval region of right atrium) were scanned using micro-CT at resolutions of 86 and 31 μm, respectively. The whole heart was then serially sectioned in the coronal plane at 50 μm thickness onto adhesive collection tape using a cryomacrotome and the SN was sectioned parallel to the crista terminalis at 30 μm thickness onto Superfrost Plus slides. Masson’s trichrome histology was performed on whole heart sections at 1 mm intervals and SN sections at 500 μm intervals. Immunolabelling of the pacemaker channel HCN4 was carried out on sister sections to help identify the tissues of the CCS. Results Many of the major components of the CCS, including SN and AVN, were identified in whole human heart sections. The PN, as well as the SN, were identified in the sections of the isolated human SN preparation. The PN appears as a region of loosely-packed myocytes in close proximity to the SN. However, the PN, whilst being in close proximity to the SN, is at no point in direct contact with it. The SN extends from the superior vena cava along the crista terminalis about a third of the distance to the inferior vena cava. In contrast, the PN is a far more extensive structure than the SN and was traced along much of the length of the crista terminalis extending from the superior to the inferior vena cava. This could be reason why the leading pacemaker site in the human can be at any point from the superior to the inferior vena cava. Avizo software is being used to align histology sections with the micro-CT data and image analysis is being used to segment the SN, PN, AVN and His-Purkinje system. Following segmentation, we will create a 3D reconstruction of the whole human heart incorporating the CCS. Conclusion We are using a novel combination of techniques to create a detailed 3D reconstruction of the whole human heart including the CCS. The 3D reconstruction will enable more accurate simulations of cardiac electrophysiology.