The three-dimensional (3D) representation of the bifurcation anatomy and disease burden is essential for better understanding of the anatomical complexity of bifurcation disease and planning of stenting strategies. We propose a novel methodology for 3D reconstruction of coronary artery bifurcations based on the integration of angiography, which provides the backbone of the bifurcation, with optical coherence tomography (OCT), which provides the vessel shape. Our methodology introduces several technical novelties to tackle the OCT frame misalignment, correct positioning of the OCT frames at the carina, lumen surface reconstruction, and merging of bifurcation lumens. The accuracy and reproducibility of the methodology were tested in n = 5 patient-specific silicone bifurcations compared to contrast-enhanced micro-computed tomography (µCT), which was used as reference. The feasibility and time-efficiency of the method were explored in n = 7 diseased patient bifurcations of varying anatomical complexity. The OCT-based reconstructed bifurcation models were found to have remarkably high agreement compared to the µCT reference models, yielding r2 values between 0.91 and 0.98 for the normalized lumen areas, and mean differences of 0.005 for lumen shape and 0.004 degrees for bifurcation angles. Likewise, the reproducibility of our methodology was remarkably high. Our methodology successfully reconstructed all the patient bifurcations yielding favorable processing times (average lumen reconstruction time < 60 min). Overall, our method is an easily applicable, time-efficient, and user-friendly tool that allows accurate and reproducible 3D reconstruction of coronary bifurcations. Our technique can be used in the clinical setting to provide information about the bifurcation anatomy and plaque burden, thereby enabling planning, education, and decision making on bifurcation stenting.