Breeding chipmunks for me was an accident. I started with two chipmunks Coby and his daughter Sue. I thought Sue needed some company and got what I was told was another female, which later turned out to be a male, Tyke. I was told I didn't have to worry about them breeding as it was quite hard, my experience has been quite different. I think if you give them enough space they will breed quite easily. If you don't want yours to breed you may have to consider keeping the males and females separate, or have the males neutered. Years ago I asked three different vets if male chipmunks can be neutered, the answer was no. Then I found the vets I use now, and they have performed the operation on all but two of my males (the un-neutered ones are a bit young still), with no bad after effects. Other people have told me they have had their males neutered without any problems, so don't be put off if the first vet you ask says it can't be done. Males are ready to mate from one year old, and can mate from January through until September. Many sources may tell you that the testicles of a male are only visible during the mating season. I found this not be strictly true, as they can retract their testicles so you may not always see them. On mature male chipmunks the testicles can be very large and dark and never retract, don't be alarmed if you notice this on your adult males.
Getting down to it
So you're going to breed chipmunks, here goes.
You need a male and a female yes that is obvious, but if your chipmunks are very young don't be so sure you have one of each sex. Remember that younger adult males can retract their testicals up in to their bodies, and only become more pronounced as they develop into an adult and in the breeding season. So you really need to turn a chipmunk upside down and take a look under the hood to be sure. If yours do not want to be held, you could try putting them in a clear plastic container to check on them (with air holes). Or, if you cannot catch yours, you can often work things out by watching them run up the side of the aviary, then you can get a good look at the underneath. The distance between the anus and the genital opening (sexual organ or papilla) is greater for males than females (about 7 to 10 millimeters on males). It can sometimes be a close call, which is why some pet shops will not guarantee the sex of the chipmunk you get from them.
The photo below is of a male chipmunk, with the genitals and anal opening shown with red arrows. This male is one year old, and you can see one of his testicles shown between the anus and genitals.
As you can see on the next photo of a female chipmunk, the distance between the anal opening and the genitals is much closer.
The next photo is another example of a male chipmunk, this one has been neutered.
The females come on heat twice a year, spring and autumn. The timing is quite varied, as this year some of my females came on heat as early as January and some are still trying to attract a mate now (it's the middle of April as I write this). One of my girls started chirping for a male for the filth time this year. The females advertise their readiness to mate by continuous chirping for the whole day. Although they must also emit pheromones, as the males will know about it even before the female starts to chirp. If your chipmunks are kept outdoors you should find they start later in the year, depending on the weather, from about March onwards.
If you have more than one male, I would recommend that you keep the pair you want to mate together for two or three days or even longer if you can, when she starts chirping. You also need to be carful of inbreeding, so remove any male siblings from her aviary, infact it would be better if you can just keep only the mating pair together, away from any other chipmunks, (more about jealously later on). Female chipmunks will attempt to mate with as many males as she can, so that's why I suggest keeping the mating pair in the same aviary, otherwise you won't really know who the father is.
They mate much the same as many other animals, the male will mount the female, and they will make a faint sort of satisfied noise as they couple. Early signs that the mating has been successfull are if afterwards (one or more days later) she may be a bit cold towards the male, or even downright hostile. But if in ten or fourteen days pass and she starts chirping again, then she is not pregnant.
If you keep any eye on her afterwards and she is pregnant you may notice she will get larger. The babies are just under her back legs, inside her body. Towards the end of her pregnancy (gestation period is about 30 days, average time) you may also notice she has developed two rows of teats along her stomach, and she may even start eating odd foods. The only time one of mine would want wax worms was when she was pregnant, and they may also start using their mineral blocks more.
Look out for different behavior on the day of the birth. It's likely you may not see the mother at all on that day, then in the first week you may only see her once or twice a day as she comes out for food. Be very careful about looking in the nest box, I would do it when the mother had come out, and only if I thought it wasn't stressing her. I would not look in the nest box for at least a week after birth, and only when the mother had come out of her own accord, and if she trusted me. You will probably be eager to know how many baby's there are and what sex.
Thankfully a baby being rejected is quite rare, although it can happen, say if it's the mothers first litter, as not all chipmunks make good mums, most do.. If you did have to bring up a very young baby chipmunk you will find it hard to find food which the baby will accept. They also need attention the first two weeks of their lives about every four hours. Use the heat from a lamp to keep an orphaned baby warm, not one of those heat lamps, unless it is quite far away. An ordinary desk lamp will work if the baby is covered with something not to heavy. If you have to feed a baby yourself as far as I'm aware there is no off the self food you can get from a vets, so you need to mix your own recipe. Nearly all the recipes contain a small amount of honey, added to condensed or evaporated milk and human baby food. You can also add some glucose powder from any chemist to the mix, then dilute it with water you have boiled and allowed to cool down to about 37 degrees Fahrenheit or 2.8 Centigrade. The mixture needs to be diluted quite well, thicken it up as the baby gets to about three weeks old, increasing the time between feeds from 4 hours to 6 after about 10 to 14 days of age. About the best thing you will find for administering the feeds is an eye dropper, but be careful not to drown the little fellow. Look out for any bubbles coming from the nostrils, if you see bubbles you're giving too much feed. Hold the baby by its back legs (never the tail) to allow excess fluids to drain. After about three weeks old I would add finely crushed rusks to the feed mix to help thicken it.
This US page explains more about bringing up orphaned babies.
Baby chipmunks cannot even pass facies themselves, the mother does this by rubbing the baby's stomach. So if you're the surrogate mum you need to do your best to replicate this action. Try using a cotton wool ball to rub along the baby's stomach from head to anus.
If possible try to keep the father in the same aviary, but provide another nest box for him, as most mothers won't allow the father to sleep in the same nest box as the babies. None of my fathers made any attempt to harm the babies, in fact some were very interested in the babies and wanted to participate in their care, whilst others were not interested at all. I found my fathers came in to play much more when the babies came out of the nest box, they seemed to treat the babies with great care, some would even want to carry them around in their mouths.
The most number of babies I've seen with my mums was seven, split between four girls and three boys. The smallest number mine have had was two, with the average being five. I believe that the factors determining litter size are the amount of space provided, the age of the chipmunk mother and if it's spring. I found larger litters born in spring, to a young mother (just over a year old).
On the whole I found most of mine made excellent mothers, but I did have one exception. She did not seem to stay with her young very much and would spend more than four hours without returning to the nest. When her babies began to crawl out of the nest she did not shown much interest in collecting them up, or seem to have much idea where they all were. With this litter I did intervene in lifting the babies back to the nest box if they were struggling with the outside world. Luckily all her offspring made it through, and some of those baby's now have a strong bond with me, probably as a result of the early human contact.
It's physically very hard work for the mum, and takes a lot out of her. So if you are going to breed chipmunks choose a female that is not too old and in peak condition. I would not recommend continuously breeding from the same female, as I have read that it can shorten a females life. I have not found any documented research to back this theory up, and have only dealt with five litters, so I can't say for sure either way. But my observations of the females bringing up a litter suggest to me that is physically demanding work for mum, so I can understand how this can be life shortening for them.
I did once have an odd occurrence which I have since found mentioned on other sites although it seems rare. One of my females abandoned her litter of two, whereupon the dominant female took over the weaning. This is the reason I now suggest that the breeding pair are kept separated from any other chipmunks you may have. As it may have been possible in this case that the dominant female forced her daughter to abandon the litter, so she could take over. What I cannot be sure of is how the dominant female produced milk, when to the very best of my knowledge she was not pregnant herself. But she did, and successfully brought up the litter of two which she had stolen from her daughter. The other reason for keeping a mating pair separate if you do have other chipmunks, is jealousy. I subsequently found out that more dominant females can view litters, which are not theirs, as some kind of threat and may kill rival litters.
I never had a problem with letting the mothers out for free range if they wanted to after she has given birth. The mums would seem to like to have a break to feed and groom themselves. Just as if they had a built in timer, they would want to go back to their babies at the right time.
For the first days you may not hear a sound from the nest box, but after a few days to a week you should notice some faint squeaking noises when the mother returns to the nest, or when she rearranges her young. On the whole they are quite silent, probably natures way of preventing discovery by predators when born in the wild.
You can expect the youngsters to want to go exploring after a month from their birth date. My mothers would often spend their time trying to pick up each of the baby's to return them to the nest. This is a bit like trying to hold back the sea if she has a large litter. No sooner has she got one back in the nest box, whilst she was busy, another three will be out for a ramble. Although the way mother may grab hold of the kids in her mouth might look a bit rough, trust her she knows what she's doing. I've seen mums deliberately step on the youngsters, often when she is trying to have a bite to eat. Stepping on them (she will press them down with one of her paws) is her crude way of keeping them still. I would sometimes help mum out if I saw she had been struggling to get a baby back to the nest for a while. In which case I would offer the mum my arm so she could choose to have a lift back. By the time my first littler arrived I had a very good relationship with the female, who knew what the presence of my arm meant. I would never try to take a baby from her, it was always her choice to take a lift up to the nest box or carry on struggling. She knows far more about bringing up chipmunks than I do.
Whilst the 're young and before they get their balancing and running around skills, it's a good chance to check over the litter, looking for any problems. They all stagger about at this age, but you can try to sex them, and look at them close up before they become too wriggly. If mums OK with you, handle them early, as this is the fastest way to tame them. Let the baby's hear your voice, and get to know your smell, gaining familiarity at an early age will take a lot of the work out of taming them later. The babies will be wobbly to begin with, and falls will happen. The youngsters are quite robust, but think about what you have on the floor of the aviary, and if they can injury themselves on anything as they fall. It can be quite worrying to see a baby take a bad tumble, so do what you can to make any landings as soft as possible. Just like humans their bones are still soft, so it's rare they ever suffer any lasting damage.
These days are absolute magic, and I found completely unmissable. I guess that's why your reading this page, because you want to experience this fascinating time in a chipmunks life. If you don't have one already, invest in a digital camera, because if it's digital you can take loads of photos. I did, but wish I taken even more at the time. I think with my first litter I was over cautious, and scared of interfering and read that the mother can reject the litter if she smelt another sent on them. I believe this to be a myth, yes it's true for other species, especially in the wild. But you are the best judge of your mums relationship with you, so don't be put off from enjoying the whole experience, its over all too quickly. I spent hours and hours watching the mums with their young, how the dads would try to get involved. Laughed at how the babies would try to follow their mum like a row of ducklings. How she would sometimes deliberately leap somewhere they could not follow her. When they caught up with mum, how they would try to dive underneath her for a feed. I should mention that you may notice your mum losing fur underneath, don't worry it happens sometimes, because of all the mauling about from the kids she's getting. The fur will grow back in time.
If it's a large litter you will probably find it impossible to tell one baby from another. With a litter size of two or three you will begin to notice their different personalities. With each of my litters I noticed there always seemed to be one or two baby's which are extremely bold. The have no reservations about you, and are up for exploring everything.
About seven weeks after their birthday the mother will want to leave them to it. In the mothers presence the babies will still head towards her when they spot her, but she can seem a bit cold towards them. Hopefully this is now fathers chance to get more involved, great if he will, but sometimes the dads just aren't interested. When my first litter was born I was lucky enough to still have grandfather Coby around. Tyke (the father was not very interested in his offspring, but Coby took an active interest in all his grandchildren). He would often be found with a little one following him around and nestled up to him. He seemed to really enjoy the youngsters from all the litters. Keep an eye on things if you do have aunts and uncles around, it's not all sweetness and light in the colony. I've read that some aunts and the dominant female can be quite jealous or feel threatened by another's babies. If given the chance, even killing a litter, presumeably to give their own litters a better chance. With mine I did feel that the aunts were capable of this, but I had no trouble from any of the uncles. I found that even the most unfriendly uncle would show no end of tolerance towards baby chipmunks from other litters. Baby's would take all sorts of liberties with an adult male, who in my case always let them get away with anything. I must stress that this is what happened with mine, but chipmunks are all so very different so keep on the look out for trouble.
In a chipmunk colony things are always changing, and I found that as they grow the playful wrestling between them changes to more serious squabbles as they establish a pecking order. I found it completely random which siblings would get on with which and which hated each other. Eventually they would even turn on their grandfather and challenge his position in the group. This was part of the reason I started getting my males neutered, I reached capacity, and I felt that introducing any more would be stressful and to the detriment of the colony. As time has passed and mine come to maturity the fights have died out, everyone has established their place, and judging by the contentment snuffles they all make I think I have a happy little family. There will always be squabbles, as one of the chipmunks thinks it's time to go up a rank, but so long as these are only minor tiffs, everything is OK.
Perhaps you can see if you plan to keep all yours, you could be fast building extra aviaries to keep them all happy. One last thing I found, I've had chipmunks that have been absolute horrors when growing up. Ones that would actively stalk and seek out their siblings and adults to pick fights. One I'm thinking of here is Izzy, he was aggressive to every chipmunk in the group, but because of his size, was only coming off worse in fights. I thought if this was someone's first chipmunk what a nasty piece of work he would seem. But I knew that once they get through their teenage years they often change for the better. I saw Izzy as a challenge, he would run away from me whenever he saw me. When I had to hold him he would take almost suicidal leaps to get away from me. It seemed as if Izzy hated everyone, the Mr Angry of the chipmunk family. But now he's already a different chipmunk, he loves life and spends nearly all day scuttling around chuckling away to himself. He's takes food from me, and just the other day jumped on my shoulder for a nuzzle. From his past battles he bears the scars, so is never going to win a beauty contest. But he's turned out to be a little bundle of fun, even has his own chipmunk friends in the group. So perhaps this is an example of changing from a chipmunk which could have played a lead role in The Exorcist to one of the extras from Disney's Bambi.