Diseases Chipmunks Carry Chipmunks are most commonly known to spread plague, salmonella, and hantavirus. Plague is a bacterial infection that attacks the immune system. It is usually transmitted via the bites of fleas carried by infected rodents. Chipmunks spread salmonella the same way they spread plague. This disease causes severe gastrointestinal discomfort and joint pain. Finally, hantavirus affects the lungs. People contract hantavirus through close contact with rodent urine or feces. If left untreated, all three illnesses can result in death. Prevention & Removal As chipmunk diseases are spread through close contact with the pest, individuals should never attempt to approach chipmunks living on their property. Do not pick up, feed, or in any way interact with the pests. At the first sign of activity, contact Critter Control to remove infestations and avoid putting house residents at risk of injury or illness.