Yet, chipmunks can be affected by and carry diseases.Examples: Eastern US ones may be a reservoir for Lyme disease (Pub Med article).In western ones Rocky Mountain Spotted Fever can be transmitted by chipmunks (NPS.gov), and also Hantavirus (google book online). California chipmunks can carry the fleas that carry the bacteria that cause plague (cdph.ca.gov).
See below for a book that discusses this: with many pictures.