The aim of this study was to examine the behavioural and cranial/spinal responses of alpacas culled by captive bolt shooting and the resulting pathophysiology of captive bolt injury. Ninety-six alpacas were shot (103 shots) in a range of locations with a penetrating captive bolt gun (CBG). Ten (9.8%) alpacas were incompletely concussed following the first shot. No animals required more than two shots. Incorrectly placed shots accounted for all of the animals that displayed signs of sensibility. Damage to the thalamus, hypothalamus, midbrain, medulla, cerebellum, parietal and occipital lobes were significantly associated with decreasing odds of incomplete concussion. In conclusion, the study confirmed that CBG stunning can induce insensibility in alpacas and suggests that the top of the head (crown) position maximises damage to structures of the thalamus and brainstem.