Rabies
Perhaps the most frightening disease carried by wild animals is rabies, a deadly illness with no known cure. Many people mistakenly believe that chipmunks and other wild rodents carry rabies. In reality, these animals rarely have rabies. In fact, a chipmunk is unlikely to develop rabies even if it is bitten by a rabid animal. Because these animals can have rabies in rare cases, it's still important to know the signs. Avoid chipmunks who are overly friendly or aggressive or who are foaming around their mouths and noses.
Disease-Carrying Insects
The biggest risk posed to humans by baby chipmunks are the insects that occasionally bite these animals or live in their fur. Chipmunks can be infested with lice and mites, both of which also infest human hair and can spread some diseases. They also frequently are bitten by ticks, which carry Lyme disease. Though chipmunks cannot spread Lyme disease to people, if the ticks in their fur jump on to people, they can be infected easily.
Infection
A bite from a chipmunk is a serious medical situation. Chipmunk bites can cause infections that, if left untreated, may lead to permanent skin and tissue loss and even organ failure. The chemicals in chipmunk saliva are foreign to human bodies, so infections are common. If you've been bitten by a chipmunk, consult a doctor and monitor the injury for signs of infection such as swelling, oozing, redness and a fever.
Parasites
Chipmunks, like most animals, are susceptible to a variety of parasites, notably roundworm. Roundworms frequently infect dogs and can also be transmitted to humans. In extreme cases, a roundworm infection can cause malnourishment and organ failure. Some chipmunks are infested with intestinal protozoa and other dangerous parasites. People who come into contact with chipmunks or their feces should thoroughly wash their hands. If your dog or cat kills a chipmunk, consult your veterinarian. Your pet could possibly develop infestations from numerous parasite species that can then be transmitted to you.