Abstract Autoimmune autonomic ganglionopathy (AAG) is an antibody-mediated form of severe autonomic failure. AAG is associated with serum antibodies against ganglionic acetycholine receptors (AChR) and appears to result from impaired synaptic transmission in autonomic ganglia. The rabbit model of experimental AAG (EAAG), induced by immunization, reproduces the cardinal features of the human disease. Pupillary dysfunction is a prominent and defining feature in both AAG and EAAG. We adapted infrared computer-assisted video pupillometry to record direct pupil light responses in control and EAAG rabbits. Offline analysis algorithms were used to determine latency, velocity and amplitude of the constriction and redilation phases of the light reflex. Following immunization, pupillary abnormalities were the earliest sign of evolving autonomic failure. EAAG rabbits showed significant reduction in velocity and amplitude of pupil constriction while redilation parameters were only mildly affected. Fatigue in pupillary constriction, evidenced by premature redilation of the pupil prior to termination of the light stimulus, was observed only in seropositive rabbits. The severity of pupillary abnormalities was significantly correlated with ganglionic AChR antibody level. In chronic EAAG, treatment with pyridostigmine produced a partial recovery of pupil function. We conclude that pupillometry is a robust and sensitive diagnostic tool to assess autonomic dysfunction, distinguish AAG from other disorders, and assess responses to therapy. In EAAG, pupillary dysfunction is partially reversible, parasympathetic pupil function is more severely compromised than sympathetic function, and fatigue of pupillary constriction may be seen. These characteristic abnormalities of the pupillary light reflex may prove to have diagnostic value.