Eye tracking is a non-invasive procedure to acquire eye-gaze data. The accuracy offered by the new eye tracking technologies gives to physicians and scientists a great opportunity to employ eye trackers to perform quantitative assessment of eye movements for diagnostic and rehabilitation purposes. However, eye trackers do not support physicians in their analysis, as they typically lack specific software solutions tailored to the diseases under investigation. For instance, ophthalmologists need to use eye trackers in tests such as visually guided saccades or smooth pursuit eye movements, while neuropsychiatrists need them in psychological tests to measure attention deficit. The development of a software tool for a specific test cannot be done by physicians (even using the high-level programming frameworks bundled with eye tracker devices) and needs to be carried out by expert computer programmers. Thus, in this paper we propose a general computer system for eye tracker – based investigation, which allows physicians to easily customize experiments in different scenarios without the need of expert computer programmers. To demonstrate the generalization capabilities of the proposed system, we show how it was employed to support the investigation of eye movements for patients affected by a) glycogen storage disease, b) idiopathic congenital nystagmus and c) neurodevelop-mental diseases such as autism spectrum disorders.