The Stomatognathic System (SS) is an integrated and coordinated morphofunctional unit, consisting of skeletal, muscular, angiological, nervous, glandular and dental structures that work in harmony to perform different functions such as chewing, swallowing, speaking, breathing, tasting and esthetics. The study of SS physiology is crucial to achieving a correct maintenance of its normal function or restoration. Thus, we developed a protocol to record mandibular movement, chewing and swallowing (saliva and water) by using the 3D-electromagnetic articulograph AG501 at the Oral Physiology Laboratory of the Research Centre for Dental Sciences (CICO). This tool has been used for decades in speech and phonetic research and it is able to record, present and evaluate articulated structure movement data in real time. The articulograph provides an ordered data matrix (values for the x, y, z axes, among others) for the recorded movement, which is stored in binary files that can be processed by different software. One of these is MATLAB®, allowing us to perform a quick, clear and understandable analysis. The existence of a standardized methodology for recording allows an accurate description of the stages to perform different types of measurements according to the researcher’s objective. This has opened the way for a new type of oral physiology analysis based on study reproducibility, which is considered one of the bases of scientific methodology.