The ethical issues surrounding slaughter as a means of control of a disease epidemic are discussed and the use of this method as at least one component of the eradication of foot and mouth disease (FMD) is justified. The Royal Society for the Prevention of Cruelty to Animals received numerous complaints of suffering at slaughter during the FMD epidemic in the United Kingdom in 2001 but none led to prosecution because of lack of evidence. Movement restrictions imposed as part of the disease control strategy caused major welfare problems on farms which were unaffected by disease. These issues are detailed. Significant breaches of transport regulations appear to have occurred.