Neurophysiological studies of anorectal function provide useful information about the integrity of innervation and neuromuscular function. This information helps to understand the pathophysiological mechanisms leading to severe anorectal disorders function, such as fecal incontinence, pelvic floor disorders and dyssynergic defecation. These tests are commonly performed in patients referred to third level medical centers having negative evaluations or no response to conventional therapy. Proper use of these tests may reveal significant new knowledge of the underlying mechanisms that can lead to better management of these disorders. These techniques are complementary to other types of research such as imaging of the pelvic floor. In this review, the most accomplished neurophysiological studies, indications and clinical utility are analyzed. Several techniques are emerging and provide us with a better understanding of the brain-gut interactions.