In internal medicine, a simple method for the functional examination of the gastrointestinal tract without the risk of radiation exposure is required. We describe a novel principle based on the monitoring of magnetic markers which meets these demands. Our method employs a special permanent magnet which is repeatedly aligned by a vertically oriented pulsed magnetic field. Due to this alignment, the marker position can be derived from the stray field components measured by commercial field sensors. Our method was evaluated by means of a 3D intestinal phantom. The monitoring procedure yielded the time course of the marker position as a 3D plot either in real-time or as a time-lapse movie. The spatial resolution, expressed by the mean square deviation, was better than 10 mm and is thus sufficiently high to distinguish between adjacent loops of the gut. The temporal resolution, i.e. the minimum time between two successive measurements, was about 1 s. The presented method has very moderate technical demands and allows us to monitor magnetic markers in real-time. The technique may be useful with respect to functional examination of the gastrointestinal tract. In pharmaceutical research, our method offers the opportunity for remote drug release at any position of the gut.