Originally an ophthalmologist (1906–12), Hess turned to the study of physiology at the University of Bonn and was appointed professor of physiology and later director of the Physiological Institute (1917–51) at the University of Zürich. He became interested in the study of the autonomic nervous system—those nerves originating at the base of the brain and extending throughout the spinal cord that control the automatic functions such as digestion and excretion. They also trigger the activities of a group of organs that respond to complex stimuli, such as stress.

Using fine electrodes to stimulate or destroy specific areas of the brain in cats and dogs, Hess found that the seat of autonomous function lies at the base of the brain, in the medulla oblongata and the diencephalon (interbrain), particularly that part of the interbrain known as the hypothalamus. He mapped the control centres for each function to such a degree that he could induce the physical behaviour pattern of a cat confronted by a dog simply by stimulating the proper points on the animal's hypothalamus. Among Hess's books is The Biology of Mind (1964).