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How To Get Rid of Chipmunks says:

The first decision you need to make when getting rid of chipmunks is whether you want to use humane or lethal techniques.

Unfortunately, the quickest and most effective ways to get rid of chipmunks are lethal to the rodents but if killing chipmunks goes against you beliefs or it is illegal to kill chipmunks in your locality, you will have to use humane methods.

The Top Lethal Method
The top lethal method of getting rid of chipmunks is to use an electric rat-trap. These traps consist of a rectangular box that you fill with bait and when the chipmunk enters, it is killed instantly by electrocution.

As well as being the most effective method, it also has the benefit of being easy to dispose of the dead chipmunk. Simple tilt the trap over your trash can an the corpse will slide it out. Because the chipmunk is killed with electricity, there is also none of the blood and gore created with more traditional traps.

The Top Humane Method
The top humane method of chipmunk removal is to use a humane chipmunk trap.

Similar to the electric trap, it is rectangular and you entice the chipmunk inside with bait but instead of killing it, the door closes behind the chipmunk, capturing it.

You can then release the chipmunk into the wild (preferably far away from your home).

Although it is more time consuming, it is a lot kinder on the chipmunk.

Other Lethal Methods
Traditional spring-loaded 'mousetraps' can also be used for getting rid of chipmunks. Because of a chipmunk's size, slightly larger traps are used than the ones used for mice and rats.

These devices kill the chipmunk by hitting them over the head with a metal bar when they try to take the bait, which in most cases causes instant death.

Another more traditional method is the 'bucket of water trap'. This is inexpensive and can be constructed at home.

Simply fill a gallon bucket with water and rest a plank of wood against it connecting the ground with the rim. Put pumpkin seeds in the water and on the plank, then leave overnight.

The chipmunk will be enticed by the bait and attempt to grab the pumpkin seeds out of the water. As it tries, it will fall in and drown.

Other Humane Methods
You can try using chipmunk repellents to get rid of chipmunks in your yard.

Although there are a number of specifically manufactured chipmunk repellents on the market, simply purchasing fox urine or scattering used cat litter around your yard can sometimes work wonders.

Mothballs are also said to repel chipmunks.

You can also try to scare them away using what is known as 'a decoy'. This is a lifelike model of a bird of prey that will at least send a shiver down the spine of any chipmunk that sees it.

How to get rid of a chipmunk says:

Trapping has always been the best way of getting rid of these critters. Google AgriZap for a cool electric trap or Google Havahart for an awesome humane trap that catches em alive.

Or you could just sit on your porch with an air rifle and pick em off one by one :)