Countless aspects of visual processing are reflected in eye movements and analyzing eye movements during visual stimulation has become the methodology of choice for many researchers in vision science and beyond. For decades, the scleral searchcoil technique has been considered the “gold standard” in terms of precision and signal to noise ratio, at the cost of pronounced setup overhead and a certain degree of invasiveness. On the other hand, camera-based eyetrackers are easy to use and non-invasive, yet, despite the dramatic improvement of the last generation systems, they have been known to be more noisy and less precise. Recently, a significant impact of changes in pupil size on the accuracy of camera-based eyetrackers during fixation has been reported (Wyatt, 2010). We compared the accuracy and the pupil-size effect between a scleral searchcoil-based eyetracker (DNI) and an up-to-date infrared camera-based eyetracker (SR Research Eyelink 1000) by simultaneously recording human eye movements with both techniques. Between pupil-constricted (PC) vs. pupil-relaxed (PR) conditions we find a subject-specific shift in reported gaze position of up to >2 degrees with the camera based eyetracker, while the scleral searchcoil system simultaneously reported steady fixation, confirming that the actual point of fixation did not change during pupil constriction/relaxation. Individual repetitions of 25-point calibration grids show the positional accuracy of the searchcoil system to be unaffected by pupil size (PC 0.52 +−0.1 deg, PR 0.54+−0.08 deg), whereas the camera-based system is much less accurate in the PR condition (PC 0.38 ± 0.12 deg, PR 0.98 ± 0.22 deg) due to increased pupil size variability. We show how these pupil-dependent shifts in recorded gaze position can affect the recorded dynamics of fixations (drift), saccades (reduced accuracy), pursuit (altered trajectory) and ocular following (directional bias), and we evaluate a dual-calibration-based method to compensate the pupil-based shift utilizing recorded pupil size.