The motility of the gastrointestinal tract is crucial for digestive activity and dysfunction can lead to severe disease pattern. A method for analysing the motility is needed when treatment approaches shall be evaluated. Therefore markers attached to different locations on the stomach and the bowel of pigs are video tracked in this research study. The markers are designed to provide a high contrast and have an adhesive side for fixation. Above the operation field a video camera has been placed to film the markers during the procedure. To analyse the video data a special algorithm has been implemented. The algorithm requires a registration process at the beginning of each recording which allows the parallel tracking of multiple markers. After the registration the algorithm tracks the position of the marker frame by frame. Each frame is converted into a greyscale picture by adding specified colour values of each pixel. This allows emphasizing certain colours. The centre of the marker is determined by computing the horizontal and vertical centre of the marker starting at the corresponding marker position of the previous frame. After completion the data is stored as coordinates and a video with the marker position displayed for further processing. For advanced analysis the data can be synchronized with electromyography signals, for example. The marked videos show a promising tracking of the markers. However, if the algorithm loses track of a marker during a recording, it is unlikely to relocate it due to the successive processing of the frames. Nevertheless this method provides a simple and easy to use solution for movement detection of the gastrointestinal tract.