The dilemma of scientific knowledge versus clinical management of TMD is discussed by focus on five questions; (1) What is scientific evidence and how is it transmitted? (2) What important evidence is lacking in the field of TMD? (3) What clinical concepts have been challenged by the scientific evidence? (4) Why is there adherence to concepts that appear to conflict with the evidence? (5) How does the clinician provide patient care in the face of uncertainty while retaining scientific integrity? It is concluded that no fundamental reason for a dilemma between scientific evidence and clinical practice need exist provided that (1) clinical investigators use appropriate research protocols and report results in refereed scientific journals and (2) dentists are familiar with the requirements of sound scientific evidence, interpret this evidence and its clinical implications, and apply it to the care of TMD patients.