Establishing the patient's clinical diagnosis depends on gathering as much information of the patient and his or her signs and symptoms as possible. This information can be gathered from history, physical and psychological examination, diagnostic analysis. It is also important to look upon pain as a disorder and to consider the relationship between pain and psychological factors. The differential diagnosis is constructed through a biopsychological model of illness rather than through a more traditional biomedical model of disease. To arrive at a consistently accurate clinical diagnosis in patients with TMJ and craniofacial pain, the technique of clinical diagnosis must be well defined, reliable and include examination of the head and the neck, cranial nerves and the stomatognathic system. The craniomandibular index provides a standardized examination of the stomatognathic system that has been tested on validity and reliability. This chapter focuses on the techniques of history taking clinical and psychological examination and diagnostic criteria for temporomandibular joint disorders and muscle pain.