The most effective ways to kill chipmunks in their burrows are snap traps placed at burrow entrances and gas cartridges inserted directly into the tunnels. Which method works best depends on how many chipmunks you’re dealing with, how close the burrows are to your home, and what your local laws allow. Here’s what you need to know before taking action.
Check Your Local Laws First
In most states, chipmunks are classified as wildlife and protected under state wildlife codes. That said, nearly every state allows property owners to kill wildlife that is actively damaging their property, even outside of hunting season and without a special permit. Missouri’s code is typical: you or someone you hire can shoot or trap damage-causing wildlife on your property to prevent further damage.
There are a few catches. You generally can’t keep or use the animal afterward. Some states require you to report the kill within 24 hours. And local city or county ordinances may restrict firearms and certain trap types within municipal limits, so check those separately. Fumigation devices and rodenticides may also require you to follow specific state pesticide regulations.
How Chipmunk Burrows Work
Understanding the tunnel system helps you target it effectively. A chipmunk digs an entrance hole about 2 inches wide, drops straight down roughly 2 feet, then tunnels horizontally for up to 10 feet before reaching a sleeping chamber. Off that main tunnel, the chipmunk excavates separate chambers for food storage, waste, and nesting.
The clever part: once construction is done, the chipmunk plugs the original entrance with dirt and opens a new, clean hole with no visible dirt mound around it. That makes active entrances harder to spot than you’d expect. Look for small, clean holes without piles of excavated soil nearby. Fresh tracks, droppings, or a chipmunk entering and exiting are the best confirmation that a hole is active.
Snap Traps at Burrow Entrances
Trapping is the most practical method for properties under an acre, which covers most residential yards. Standard rat-sized snap traps work well for chipmunks and kill quickly.
Place traps directly next to active burrow openings or along runways where you’ve seen chipmunks traveling. Peanut butter, sunflower seeds, or nuts all work as bait. To figure out how many traps you need, do a quick count of the chipmunks you can see at one time and multiply by three. If you spot two chipmunks, set six traps. This accounts for animals you’re not seeing and gives you enough coverage to make a dent quickly.
Expect to do follow-up trapping. Chipmunks from surrounding areas will move into vacated territory, so you may need to keep traps active for a week or two after you stop catching anything.
Gas Cartridges for Burrow Fumigation
Gas cartridges are designed to be lit and pushed into active burrows, where they release high concentrations of carbon monoxide as they burn. The standard formulation is 65% sodium nitrate and 35% charcoal, which together create a lethal gas that fills the tunnel system.
The basic process: confirm the burrow is active, then find all visible openings. Puncture the cartridge cap at the marked points, insert the fuse, and light it. Push the lit cartridge as deep into the burrow as possible, fuse-end first, then immediately seal the entrance tightly with soil. If the burrow drops steeply, place the cartridge with the fuse end pointing up so the burning contents don’t spill out. Seal every other opening you can find to prevent gas from escaping.
Safety Restrictions
Carbon monoxide is colorless and odorless, and exposure can be fatal to humans within minutes. These devices cannot be used inside any structure, and most state regulations require a minimum setback distance from any building inhabited by people or livestock. The exact distance varies by state and by the type of rodent being targeted, so check your state’s pesticide regulation agency for specifics.
Before fumigating, inspect the burrow system carefully. You’re required to confirm that no non-target animals are using the tunnels. Chipmunk-sized holes can also shelter snakes, frogs, or other small wildlife. A portable borescope (a small camera on a flexible cable) can help you look inside before treating. Fumigation is prohibited on any burrow that may contain non-target species, including threatened or endangered animals.
Why Poison Baits Are Risky
Rodenticides are technically registered for use against chipmunks, since the EPA classifies chipmunks as rodents alongside rats, mice, and squirrels. But poison baits create serious problems that traps and fumigation don’t.
The biggest concern is secondary poisoning. A chipmunk that eats anticoagulant bait doesn’t die instantly. It moves around for hours or days, getting slower and easier to catch. Any predator that eats that chipmunk, whether it’s your cat, a neighborhood dog, a hawk, or an owl, ingests the poison too. National Park Service monitoring in one region found anticoagulant exposure in 92% of bobcats, 83% of coyotes, and 94% of mountain lions tested. Poisoned rodents pass toxins all the way up the food chain.
The EPA has responded by restricting the most toxic active ingredients on the consumer market and requiring bait stations in sensitive areas. Strychnine, one of the more effective burrowing rodent poisons, can only be used below ground, and products above 0.5% concentration are restricted to certified pesticide applicators. For a homeowner dealing with a few chipmunk holes in the yard, the collateral risk of poison baits rarely justifies using them when traps work just as well.
Practical Approach for Most Yards
For a typical residential property with a handful of active burrows, snap traps are the simplest and safest starting point. They’re inexpensive, don’t require any special licensing, and kill instantly without introducing toxins into your yard. Set them in the evening when chipmunks are heading underground, and check them every morning.
If you’re dealing with a larger infestation or burrows are undermining a foundation, retaining wall, or paved surface, gas cartridges are more efficient since they treat the entire tunnel system at once. Just respect the setback distances from buildings and confirm the burrows are active before lighting anything.
Whichever method you choose, persistence matters more than technique. Chipmunks reproduce quickly, with litters of two to eight pups, and neighboring chipmunks will colonize empty burrows. A single round of control often isn’t enough. Plan to monitor and re-treat for several weeks until you stop seeing new activity.