Augmentation of endoscopic video with preoperative or intraoperative image data [e.g., planning data and/or anatomical segmentations defined in computed tomography (CT) and magnetic resonance (MR)], can improve navigation, spatial orientation, confidence, and tissue resection in skull base surgery, especially with respect to critical neurovascular structures that may be difficult to visualize in the video scene. This paper presents the engineering and evaluation of a video augmentation system for endoscopic skull base surgery translated to use in a clinical study. Extension of previous research yielded a practical system with a modular design that can be applied to other endoscopic surgeries, including orthopedic, abdominal, and thoracic procedures. A clinical pilot study is underway to assess feasibility and benefit to surgical performance by overlaying CT or MR planning data in realtime, high-definition endoscopic video. Preoperative planning included segmentation of the carotid arteries, optic nerves, and surgical target volume (e.g., tumor). An automated camera calibration process was developed that demonstrates mean re-projection accuracy (0.7±0.3) pixels and mean target registration error of (2.3±1.5) mm. An IRB-approved clinical study involving fifteen patients undergoing skull base tumor surgery is underway in which each surgery includes the experimental video-CT system deployed in parallel to the standard-of-care (unaugmented) video display. Questionnaires distributed to one neurosurgeon and two otolaryngologists are used to assess primary outcome measures regarding the benefit to surgical confidence in localizing critical structures and targets by means of video overlay during surgical approach, resection, and reconstruction.