Here we introduce a new video-based real-time eye tracking system suitable for functional magnetic resonance imaging (fMRI) application. The described system monitors the subject's eye, which is illuminated with infrared light, directly at the headcoil using an endoscopic fibre optical system. This endoscopic technique assures reliable, easy-to-use and fast adjustment. It requires only a minimal amount of equipment at the headcoil and inside the examination room. Moreover, the short distance between the image acquisition optics and the eye provides high spatial tracking resolution. Interference from physiological head movement is effectively reduced by simultaneous tracking of both eye and head movements.