Since decades, the dental profession has been challenged by pain and dysfunction of the masticatory system. In recent years, a better understanding of the pathophysiological mechanisms of masticatory pain paralleled the increase of basic and clinical research focusing on pain in general. Consequently, so-called diagnostic techniques and treatment procedures, based upon hypothetical, sometimes dogmatic, etiological mechanisms, are increasingly questioned, and the ill-supported thoughts are gradually replaced by research-based insights. In addition, a better communication between basic scientists, researchers, and medical or dental practitioners focusing on musculoskeletal pain, has led to an improved quality of research on pain and dysfunction of the masticatory muscles and the temporomandibular joint (TMJ). This paper will try to review this progress, comment on the clinical implications, and give some suggestions for future research.