There are nearly as many preferable habitats for the various types of chipmunk as there are differences between them. Which is easily understood considering they inhabit elevations ranging from sea level to 14,000 feet and their corresponding eco-systems. One habitat characteristic that seems to be common among many types of chipmunk is the preference for some sort of rocky outcropping which is used for both burrow creation and shelter. Other chipmunks prefer forested areas, and for a few types, the forest is a requirement for their habitat. Others still, strictly avoid it.

Most chipmunk burrows will be 20 to 30 feet long and have many openings, some of which may be hidden by leaves and debris. The burrow system will typically contain a nesting chamber and several food storage chambers and may be used for many seasons. In the creation of the burrow system, the chipmunk does not leave any apparent dirt mounding near any of its burrow openings; it will carry this dirt away in its cheek pouches and loosely distribute it to help conceal these entrances.

The least chipmunk, Allen's chipmunk, red-tailed chipmunk, long-eared chipmunk, Merriam's chipmunk (the Unita chipmunk and Palmer's chipmunk as well, to a lesser extent) all are prolific climbers and often will construct their nests in a tree high above the ground. Most of the other members of the species' not listed above are only found in a tree when frightened. All chipmunks create their hibernation chambers underground.

Particular preferences for individual species may be found below. Not all species are listed:

• Eastern chipmunk - A ground dweller. The eastern chipmunk has two breeding seasons a year averaging 4 to 5 offspring per pregnancy. This chipmunk will defend a small territory around its burrow.
• Least chipmunk - An occasional Tree dweller. The least chipmunk has one litter a year of between 2 and 6 young. The male of this species may help raise the young.
• Colorado chipmunk - A ground dweller that may often be seen foraging for food high in trees. This chipmunk can be found at elevations from 6,000 to 8,200 feet. The Colorado chipmunk typically has one litter of 2 to 7 young per year, however, a second litter occasionally may be found in the late fall. The male of this species may help raise the young.
• Uinta chipmunk - A tree dweller found at elevations from 6,500 to 11,200 feet. The Unita chipmunk has one litter of 4 to 5 young per year. This chipmunk may occasionally create its nest in an abandoned birds nest.
• Lodgepole chipmunk - Another ground dweller that may often be seen foraging for food high in trees. The lodgepole chipmunk will have one litter of 3 to 6 pups per year. This chipmunk can be found at elevations from 4,900 to 11,000 feet. A very shy chipmunk that will rarely be seen or heard.
• Sonoma chipmunk - A ground dweller. The Sonoma chipmunk has one litter of 3 to 5 young per year. This chipmunk can be found at elevations from sea level to 6,000 feet. It is generally believed that the members of this species found at lower elevations do not hibernate.
• Allen's chipmunk - A tree dweller found at elevations from 500 to 6,000 feet. The Allen's chipmunk has one litter of 3 to 5 young per year.
• Red-tailed chipmunk - Another tree dweller. The red-tailed chipmunk has one litter of 3 to 8 young per year.
• Long-eared chipmunk - A tree dweller found at elevations from 3,200 to 7,400 feet. The long-eared chipmunk has one litter of 3 to 5 young per year.
• Panamint chipmunk - A ground dweller preferring a rocky habitat. The Panamint chipmunk has one litter of 4 to 6 young per year and will be found at elevations between 4,500 and 9,000 feet.
• Palmer's chipmunk - Mainly a tree dweller found at elevations from 6,900 to 11,800 feet. The Palmer's chipmunk has one litter of 3 to 6 young per year. This species of chipmunk is extremely aggressive and territorial.
• Merriam's chipmunk - A tree and ground dweller found at elevations up to and beyond 8,800 feet. The Merriam's chipmunk has one litter of 3 to 7 young per year.
• Cliff chipmunk - Typically a rock outcropping dweller found at elevations from 4,900 to 12,000+ feet. The Cliff chipmunk has one litter of 4 to 6 young per year and is usually active in the early morning and late afternoon. This species of chipmunk is fiercely territorial near its burrow but often shares food sites with other cliff chipmunks.
• Gray-collared chipmunk - A ground dweller found at elevations from 6,400 to 11,000+ feet. The gray-collared chipmunk has one litter of 2 to 5 young per year. These animals will often be found around homes and structures.
• Gray-footed chipmunk - A ground dweller found at elevations from 5,300 to 11,900 feet. The gray-footed chipmunk has one litter of about 4 young per year.
• Yellow-pine chipmunk - A tree and ground dweller found at elevations from 2,000 to 14,000+ feet. The yellow-pine chipmunk has one litter of 3 to 8 young per year.
• Alpine chipmunk - A ground dweller found at elevations from 7,500 to 12,500+ feet. The alpine chipmunk has one litter of 4 to 5 young per year.