Endovascular procedures are characterised by significant challenges mainly due to the complexity in catheter control and navigation. Real-time recovery of the 3-D structure of the vasculature is necessary to visualise the interaction between the catheter and its surrounding environment to facilitate catheter manipulations. State-of-the-art intraoperative vessel reconstruction approaches are increasingly relying on nonionising imaging techniques such as optical coherence tomography (OCT) and intravascular ultrasound (IVUS). To enable accurate recovery of vessel structures and to deal with sensing errors and abrupt catheter motions, this letter presents a robust and real-time vessel reconstruction scheme for endovascular navigation based on IVUS and electromagnetic (EM) tracking. It is formulated as a nonlinear optimisation problem, which considers the uncertainty in both the IVUS contour and the EM pose, as well as vessel morphology provided by preoperative data. Detailed phantom validation is performed and the results demonstrate the potential clinical value of the technique.