The term ‘depopulation’ is used in this case to describe mass euthanasia or killing of groups of animals on a farm for emergency disease eradication purposes. There are a number of guidelines for monitoring animal welfare during such operations, eg the OIE Terrestrial Health Code and the EU regulation on protection of animals at the time of killing, which can be useful when designing a specific monitoring system for depopulation. In this paper, the responsibilities of the competent authorities are identified, and a systematic approach to monitoring on-farm killing is proposed, including three major critical points: i) animal handling prior to killing; ii) the stun/kill quality, ie the effectiveness of the method used to render the animals unconscious and dead; and iii) confirmation of death prior to carcase disposal. The importance of good biosecurity routines, efficient disease detection systems, relevant training of staff and thorough contingency planning to prevent animal welfare problems from arising is strongly emphasised. It is the responsibility of national competent authorities to provide the appointed official veterinarians in charge of monitoring animal welfare during depopulation with proper tools, including anything from appropriate knowledge and practical checklists to the authority to demand immediate corrective action when necessary, and to develop systems for feedback and incorporation of experiences from previous outbreaks into the national contingency plans.