OBJECTIVE: To establish a workflow integrating preoperative 3-dimensional (3D) angiography data and intraoperative real-time vascular information in microscope-based navigation for aneurysm and arteriovenous malformation (AVM) surgery. METHODS: In 7 patients (3 with AVMs and 4 with aneurysms), preoperative 3D rotational angiography or computed tomography (CT) or magnetic resonance angiography data were navigated applying a 32-slice movable CT scanner for low-dose registration scanning. The 3D vasculature was segmented and visualized by microscope-based navigation along with navigated intraoperative real-time imaging data from indocyanin green angiography and duplex ultrasonography. RESULTS: Automatic registration applying intraoperative CT resulted in high accuracy (registration error, 0.80 ± 0.79 mm). The effective radiation dose of the registration CT scans (0.28-0.42 mSv) was only approximately one-sixth of a standard diagnostic head CT scan. The 3D vessel architecture could be visualized accurately in the operating microscope heads-up display and on the navigation screens in the same projection as the view angle of the surgeon, both facilitating orientation in 3D space, providing a better understanding of anatomy. In addition, intraoperative real-time modalities could be coregistered with high precision, providing further information during the course of the vascular procedure. CONCLUSIONS: Registration CT imaging facilitates integrating preoperative and intraoperative vascular image data with a low registration error and low radiation exposure for the patient, improving the understanding of 3D vascular anatomy during surgery with easier identification of feeding vessels in AVMs, and of the projection and configuration of aneurysms.