A system for automatic detection of eye movements in medical applications is presented. It is designed to register exactly the dynamic motions of human eyes. In principle, the system runs independently of specific applications and may be used for different medical diagnoses. The method for motion analysis is applied to video image sequences of the retina recorded by a scanning laser ophthalmoscope (SLO). A modified block-matching algorithm has been developed for tracking the ocular fundus in the SLO sequences. The image processing strategies implemented provide high reliability of the motion detection which is used to process off-line. Several modifications have been developed in order to take into account the video quality of the SLO sequences. Additionally, some improvements have been implemented to increase the speed of the software. The system includes a phase of automatic motion detection followed by a subsequent phase of manual quality control. In this latter phase, an efficient tool for error detection and correction guarantees high quality and security of movement detection, which is of great importance in clinical applications.