Overall chipmunks are very hardy little animals - most live long lives, dying of old age. The greatest cause of chipmunk illness appears to be a result of improper diets, the next greatest being dangerous environments. A chipmunk needs a food dish; a ceramic one is best as they cannot tip it over. In addition to that there needs to be a constant water source in the form of a dish or bottle. It is important to keep the water filled, and to clean feeders often. A chipmunk should have about 28 grams of food a day, less if an aged chipmunk.
I tend to give more food less often; I fill the dish then leave it for two days or so. My animals tended to take their favorite things and try ignoring the healthier items, knowing the next day more would come. By leaving them longer they are forced to eat healthily foods instead of constantly picking and choosing the more unhealthy treat-like items they prefer. Sometimes this must be done, but if your animal has an empty dish, fill it. Whatever is not eaten usually is hidden in a cache, sometimes under cage bedding or in their nest box. Most chipmunks do this behavior and it should not be discouraged as it is a natural process. Even though a pet chipmunk, constantly given the same supply of food, doesn't need to store up food, it does anyway; It's just instinct.
Here I will list what you need in general, why you need it, and how you can get it into your chipmunk's diet. This is my own dietary base but for every chipmunk owner there is a different idea of what is best. Many owners find that due to their own research they discover reasons why/why not have something and modify the diet as necessary - so be prepared to do some study! Remember, this is an animal that has not had a diet perfected so there is no 'perfect diet' for a chipmunk. Read up and study all sorts of expert opinions and pet owner opinions. The only certain fact is that a chipmunk needs a variety. Most pets are given one food item, but this will not work for a chipmunk. Having two dozen types of food on hand would be a good idea.
Obviously items like junk food, candy and chocolates are inappropriate; Processed sugar is as near a death sentence as you can get for a chipmunk. Due to this reason double check the ingredients list on EVERYTHING you buy - sometimes what is labeled as 'natural' or 'organic' still gets a heavy dousing of sugar. When feeding fresh foods avoid pesticides. Better to be overly cautious than to fed your animal something toxic that will cost them their life.
The greatest thing you can do to prevent health problems is to carefully prepare a healthy diet. This can be difficult due to the lack of scientific study on their care. It does not help that there are many conflicting reports between those who actually own chipmunks on what is best, too. Throw yourself into doing your own research, difficult as it might seem, knowing that it will be a lifetime benefit to your animal.
Staple: Forms the base of the diet. Main source of energy and the source for most necessary foodstuffs, vitamins/minerals - something that 'covers it all'. Most cats/dogs are only fed a singular staple item (like kibble).
Most people use store-bought hamster pellets for chipmunks, as they are convenient (available at almost every pet store and a bagful is cheap). Some owners are sure to only buy vegetarian blocks, some bypass them entirely due to cornmeal/peanut content, other nutritional concerns, or other reasons, like the process of extrusion. You can also use bread (Not talking white/wheat!); The bread I mention is a specially made squirrel/chipmunk bread, made specifically for their dietary needs, although most people do call them 'blocks'. They can be found for sale here and are healthier and tastier for our chipmunks. I like to make my own (recipe on TSB forum) & adjust ingredients, depending on who is eating it!
Grains & Seeds: Good source of carbohydrates, fiber, B-vitamins, iron, magnesium, zinc, copper, manganese, selenium. Provides energy, aids digestion and provides many of the necessary vitamins/minerals. Popular pet grains/seeds are oats, barley and sesame seeds.
Oats, wheat, rye and barley are fantastic grains that are cheap in volume and loved by chipmunks. Avoid putting sunflower seeds, corn, & any nuts into this category! We will get to those later on.
You can find these items in a natural or organic foods section of supermarkets. Be sure to check the ingredient list to make sure there are no additives. Certain biscuits work well too (some chipmunk owners give dog biscuits!).
Fruits & Vegetable: This next part is easily self explanatory - fruits and veggies! These healthy snacks are important for chipmunks who need their fiber, potassium, and vitamins (like C or D). They are also great sources of water.
I find it easiest having a few kinds of dried fruit/veg around (pineapple, papaya, mango, apple, and many more), but watch that they aren't the sort with added sugar. Usually it is best to give vegetables with the basic meal and to generally treat fruits like treats in that they should be given more sparingly. It is a chip-tastic idea to take a tiny bit of whatever fresh fruit or vegetable from your dinner table and share it with your chipmunk twice a week (a bit of lettuce, carrot, etc). Make sure any fresh food has been washed and that nothing you feed them is processed. Avoid anything with pits too, as those contain a chemical that can prove toxic when digested. Here is a great list of no-no’s (Plant List), bearing in mind it is for all exotics in general and is not a chipmunk-specific list. Check any item thoroughly (by running the name through lists, checking chip-sites and forums) before you give it to them for the first time!
Calcium: Most people do not think rodents need this and that a diet of only seeds and nuts is fine - WRONG! Just like every other animal chipmunks need strong bones! A lack of this results in an unhealthy chipmunk, commonly MBD, sometimes even death.
The most popular form of calcium for chipmunks is yogurt, and the easiest way to give that is either as yogurt bites/drops or yogurt covered raisins. It's also delightful to sit holding a spoon and watch your chipmunk lick the yogurt. Stick with organic yogurt, something natural and not heavily processed or loaded with added sugar. You can also give them rosehips (available for purchase over the internet but I’ve yet to see them in stores). Some leafy greens will give large amounts of calcium and vitamin D, too. Some people find the dairy need inconvenient and instead add supplements (See below).
Protein: Protein is found in many pellets so giving another kind is not always necessary but I encourage it and my animals seem to enjoy it. Protein aids enzymes and muscles, especially in repair. Most high protein items are a necessary source of fatty acids (omega-3s) and vitamin E.
Protein is found in high content in nuts and meat. Crickets and mealworms are favorites of my own chipmunks, but other insects work well too. You can even feed a cooked egg. A lick here or there of organic peanut butter is a satisfying treat, but should be limited (fat content).This is sometimes seen as optional as many chipmunks live strong and healthy lives without ingesting any animal matter and get by on pellets/nuts, though these should be considered treats (see just below).
Other: These are foods that we as humans do not consider food, however they are eaten by chipmunks and are a necessary part of their diet.
These include certain types of bark/sticks (fruit tree), flower petals and other plant parts, some bone like deer antlers or cuttle bone.
Many can be found in your own backyard, or for sale over the internet/in a pet store. Fruit tree bark should always be pesticide free, and be cleaned/heated beforehand to remove pests if taken from the wild. Hibiscus, Marigold, Dandelion, etc flowers are appealing as are stems/leaves of some plants. In the wild this (stems/plants) would make up a much larger part of the diet than it would as a pet. Deer antlers, cuttle bone, and even sea shells, are all full of minerals and calcium. NOT EVERY PLANT IS SAFE - MANY ARE TOXIC - CHECK EVERYTHING BEFORE FEEDING TO YOUR CHIPMUNK!
Treats: These are all the things that, if given a chance, your chipmunk would eat from their dish first while leaving everything else behind (like giving your child the option of a cookie or broccoli - which will they go for isn't hard to guess). It is best to only use treats to get close to your chipmunk - every treat should leave your fingertips; Food is a bonding material. All negative effects of treats should already be canceled out in the regular diet. Be sure not to overdo treats or there could be a health risk. Most outdoor/wild chipmunk feed (Sunflower seeds and corn) is too high in fat for pets and would be a once a month treat for a healthy pet and should never be used as a staple diet for a pet chipmunk.
Treats should be fed sparingly, and always given when you bond with your animal. Not all 'treats' are the same, meaning some are 'dangerous' (very bad phosphorous/calcium ratio, too high in fat, etc) and those 'dangerous' ones should be given rarely (once a month) or avoided altogether. A kernel of corn each month is advantageous to building a silky coat in chipmunks and a healthy layer of fat, but too much results in an overweight chipmunk in time so generally avoid it (making it a dangerous treat). Most nuts fall into the category of treats (Hazelnuts, almonds, acorns, peanuts, etc) as well as some seeds (Sunflower or pumpkin seeds) due to the high quantity of fats or phosphorous (all vary in 'danger' level - consider both those seeds once a month treats or off limit items). Waxworms also fall into the treat category.
I have found that the more research you do, the more the diet changes. The greatest informational resource I found was this website, TPSB.
Many people find that they want to add to their pet's diet to be sure it is getting all the necessities. You can buy specific vitamins and minerals for squirrels/chipmunks (found over the internet, most pet stores are nowhere near stocking anything chipmunk related unless they sell them, and few do) or find a specific supplement for a single dietary deficiency. Your best option is to study up on diet and understand what you are feeding, and why. Try and have a complete diet before you turn towards supplements (with the exceptions of mineral blocks/cuttle bones - always have those). If you still feel your diet is pretty snazzy but missing "just one thing" you can buy specific supplements - most people seek calcium or minerals. You can buy drops to put in water to give calcium or powder to sprinkle over food, or leave a cuttlebone inside the cage for the animals to gnaw. Minerals can be added most easily in the form of a hanging mineral block left in the cage (You can also use bee pollen).
Supplements are fine if you know what your animal is lacking and how much. Some people don't and over/under dose their animals. How much does that one drop really translate to? Add a powder/drop supplement only if you really know that the amount you are giving is the one needed; Otherwise you may give too much, and there are certain things that ARE toxic in high volume (like vitamin A) so one must be prudent.
If you are on your first chipmunk or are fairly uncertain of how much of a supplement you would need it might be a better idea to buy items hanging on the sides of cages, or blocks, like cuttlebone, mineral blocks (Manu), 'fortified chews'. With a source at the ready, the animal has the option to take in the mineral/vitamin whenever they feel it is needed rather than us guessing.
I find it useful to leave both a cuttlebone and mineral block in each cage at all times, so that the animal has the option to take in extra at it's leisure, whenever they feel it is needed (they'll know their own bodies better than we ever will!).
A note on mineral stones, cuttle-bones, and other items hung on cage walls:
You might put this in and then not think about them until you notice they haven't been used.. Don't worry! Chipmunks know when they need something. You might find they don't touch it for months, then jump on it. If unused, do not remove them!