Designing classification systems and developing diagnostic criteria for temporomandibular disorders is difficult. An appreciation of the utility and applicability of these entities requires an understanding of the importance of each, the differences between the two, and how they may be optimally operationalized for both clinical and research activities in light of their inherent advantages and limitations. In addition, consideration for adopting newer approaches, such as following ontological and precision-based medicine principles, accounting for genetics/epigenetic and neurobiological factors, and the inclusion of biomarkers will potentially result in more thorough and comprehensive classification systems and diagnostic criteria.