Carnaby's Cockatoos (Calyptorhynchus latirostris) are in decline in SW Western Australia from several processes, including habitat loss and fragmentation. However, in recent years, a disease syndrome has also emerged as a significant population threat. Emerging diseases in wildlife have the potential for catastrophic effects on population numbers, especially if a species is experiencing existing pressure from other threatening processes. This article describes an investigation into a hindlimb paralysis syndrome that has occurred in the summer and autumn since 2012 in 84 wild Carnaby's Cockatoos. Recovery from the syndrome has been demonstrated in 21 of 33 cases when supportive therapy was applied. Although a definitive diagnosis has not been obtained, the hypothesized etiology is an organophosphate-induced delayed-onset neuropathy. The syndrome may indicate that interaction between the cockatoos and inland agricultural practices are affecting this migratory species in ways that are, so far, poorly understood.