Alterations in breathing, chewing and swallowing are considered risk factors for functional disorders on the stomatognathic system. Thus, there is a need to have a protocol for functional evaluation that contributes to systematize the processes and procedures, unifying criteria for diagnosis. The objective of this study was to design a Protocol for the functional evaluation of the stomatognathic system for the Postgraduate Clinic of Orthopedics of the School of Dentistry of the University of Zulia, Venezuela. In a first stage, a situational diagnosis was made. In a second stage, the documentary analysis technique was used, using the search engines Pubmed, Redalyc, SciELO and ScienceDirect. The third stage consisted in the elaboration of the protocol according to the consensus of the resident postgraduate professionals and the evidence found in the review of the scientific literature. The protocol was drawn up, defining its objectives, population, institutional resources and a systematic and detailed ordering of the procedures and tests to be applied for the evaluation of breathing, chewing and swallowing. This protocol will improve the quality of the evaluations and obtain reliable records of the patient’s clinical condition.