Since the early 1970s, coronaviruses have been recognized as causing pathological conditions in veterinary medicine. the major related diseases have mainly an intestinal location with the exception for avian infectious bronchitis. Coronaviruses primarily infect the upper respiratory and gastrointestinal tract of birds and mammals. They also cause a range of diseases in farm animals and domesticated pets, some of which can be serious. The infectious bronchitis virus (IBV) targets not only the respiratory tract but also the urogenital tract in chickens. The virus can spread to different organs throughout the chicken. Economically significant coronaviruses of farm animals include bovine coronavirus and porcine coronavirus (transmissible gastroenteritis coronavirus, TGE). These coronaviruses both result in diarrhea in young animals.

Feline enteric coronavirus is a pathogen of minor clinical significance. However, spontaneous mutation of this coronavirus can result in feline infectious peritonitis (FIP) which is associated with high mortality in cats. In ferrets, there are two types of coronavirus, the ferret enteric coronavirus (FEC) and the ferret systemic coronavirus (FSC). The ferret enteric coronavirus causes a gastrointestinal syndrome known as epizootic catarrhal enteritis (ECE). The ferret systemic coronavirus is a more lethal systemic version of the FEC.

There are two types of canine coronavirus, one that causes mild gastrointestinal disease and one that has been found to cause respiratory disease. Mouse hepatitis virus (MHV) is a coronavirus that causes an epidemic murine illness with high mortality. A progressive demyelinating encephalitis is caused in mice by some strains of MHV. The mouse hepatitis virus had been the best-studied coronavirus before the discovery of SARS-CoV.

Laboratory rats are regularly infected by the highly infectious coronavirus Sialodacryoadenitis virus (SDAV). This virus can be transmitted between individuals by direct contact and by aerosol transmission. Acute infections have high morbidity and tropism for the salivary, lachrymal and harderian glands. The swine acute diarrhea syndrome coronavirus (SADS-CoV) is related to the HKU2-related bat coronavirus and causes diarrhea in pigs.