The trigeminal nerve and nuclei (the trigeminal complex) are unique in the human body with regard to their anatomical and physiological characteristics. They are also special regarding the lesions in which they are involved, both at the peripheral level because of the susceptibility of some terminal branches, and at the nuclei because of their large size and the large amount of connections with other centers. Conventional magnetic resonance imaging studies are often not sufficiently informative to demonstrate very tiny lesions that could be responsible for an important damage in the brainstem. Therefore, clinical neurophysiology and specifically, the techniques used in the study of the trigeminal functions, remain as convenient diagnostic and research tools to document clinically evident lesions or uncover subclinical abnormalities. This review is focussed on the clinical applicability of the study of trigeminal reflexes, including methods employed in the documentation of focal lesions of peripheral branches, trigeminal involvement of peripheral neuropathies, specific lesions of the trigeminal ganglia, central nervous dysfunctions causing abnormalities in the excitability of trigeminal neurons, and the possible use of trigeminal nerve reflexes in the study of facial pain syndromes and headache.