The chipmunk is not considered to be the source of any sort of significant personal or agricultural damage. Trouble with these animals will usually arise if they create a burrow near or under a structure or through sporadic "digging up" of landscaping plants or bulbs. Concern is warranted when a great numbers of these animals create burrows near or under a structure, patio, retaining wall, or sidewalk as the voids created by these burrows can cause structural failure.

Some species of chipmunk have been found to carry disease and disease carrying insects. Keeping these animals (or any wild animal) isolated from human and pet populations through the use of preventative measures is always considered a best practice.

A large population of chipmunks may affect forest growth by excessive seed consumption.