Vaccinating can be a lifesaving procedure, but it is a medical intervention that is not without risks.
Many animals in shelters have not had natural or vaccine exposure to common diseases, so the benefits of immediately vaccinating on entry almost every animal over four weeks of age typically outweigh the risks. Those early vaccinations can create a "herd immunity" in which the vaccinated majority will provide protection for individuals who have not developed immunity. That can limit the impact some diseases may have on the health of the overall animal population.
Here is information to help you make decisions about vaccinating special shelter populations. In all these cases, consult your shelter veterinarian for specific concerns.
In general, it is best to vaccinate only healthy animals since a healthy immune system can respond better to a vaccine. However, many animals enter the shelter who are not in ideal health, and the risk of not vaccinating may be potential exposure to life-threatening disease.
Experts advise that animals with common, mild illness (such as minor upper respiratory disease) still receive vaccines. Your veterinarian can help determine a protocol that works best for your shelter, but a safe guideline to follow is if an animal has a fever over 103.6, the vaccine may not work and the animal should not receive it. Consult your veterinarian in all cases of unusual illness and where an animal has a high fever.
There are no vaccine risks to nursing cats and dogs, so vaccination is recommended. Kittens and puppies can receive their first subcutaneous vaccines at 4-6 weeks of age and there is no risk to the babies when nursing moms are vaccinated.
There are some risks to unborn kittens when using modified live vaccines, especially at certain stages of gestation. The risk to unborn puppies is much less well understood.
The ASPCA recommends that shelters consider the risk of infectious disease to pregnant animals when weighing vaccination decisions. In many cases where disease risk is significant, vaccination is advised. If animals will soon be spayed, vaccination is also advised. If disease risk is low, foster is immediate, or legal status is uncertain, vaccination might best be delayed.
In most cases, vaccinating injured animals is the suggested course of action, especially if the injury is not severe. When making difficult vaccination decisions, it's best to consult the veterinarian your shelter works with and consider the overall benefit and risk to each individual animal as well as the shelter population as a whole.