The aim of this study is to propose a new semi-automated method for three-dimensional (3D) reconstruction of coronary bifurcations arteries using X-ray Coronary Angiographies (CA). Considering two monoplane angiographic views as the input data, the method is based on a four-step approach. In the first step, the image pre-processing and the vessel segmentation is performed. In the second step the 3D centerline is reconstructed by implementing the back-projection algorithm. In the third step, the lumen borders are reconstructed around the centerline to result to the fourth step, during which the 3D point cloud of the side branch is adjusted to the main branch, to produce the final 3D model of the coronary bifurcation artery. Imaging data from seven patients (pre and post-stenting) were reconstructed in the 3D space. The validation of the proposed methodology was based on the comparison of the 3D model with the 2D CA. Blood flow simulations were performed both for the vessels before and after the angioplasty procedure. Decreased Endothelial Shear Stress (ESS) values were observed for the vessels after the Percutaneous Transluminal Coronary Intervention (PTCI).