When your chinchilla comes up with diarrhea, there are a couple things you should do. First, ask yourself: is this new, or has this problem been going on for a while? Know your chinchilla's rhythms, and know if this is an indication of an ongoing problem. Diarrhea can be a symptom of many things. If this is an ongoing problem, then check with your vet, and do what you have been doing.
If the diarrhea is a new condition, you should have your chinchilla checked by a vet, particularly a vet experienced with guinea pigs and other rodents. Have your chinchilla's stool checked under the microscope as a wet mount [it must be fresh] for giardia and coccidia. Have your vet check the teeth [which takes a lot of finesse], making sure that the molars do not have spurs or points. If they do, they need to be burred down - a procedure best done under anesthesia. If your animal has giardia, then ask for Albendozol, not Flagyl. Flagyl is still the only accepted treatment for giardia, but unfortunately it kills no more than 50% of the parasite and has been implicated in liver failure in chinchillas. Albendozol, however, usually does kill the bug after 3 days of treatment and does not seem to have bad side effects because it is not absorbed into the blood stream. It does sometimes cause a little loss of appetite for a couple of days, but this usually passes.
If none of the above is present. Then give the chinchilla some Kaopectate for children. Cherry flavor seems to be most favored. Pour some into a teaspoon, and let your chinchilla lap up as much as it wants. If one or two doses in one or two days does not cure this, try some yogurt with a little Metamucil. Mix about 1/4 teaspoon into an ounce of yogurt and give to your chin. If this does not help, and the diarrhea persists, have a longer exam by the vet including a complete blood count. Sometimes coccidia does not show up under the microscope but it can cause anemia because it causes hemorrhage.
While this is going on, go to a basic diet: pellets and hay only and a lot of water. You need to replace fluids your chinchilla is losing. You might want to put some Pedilyte into the water for electrolytes. Weigh your animal daily. If it is losing weight, then switch to alfalfa and grind up pellets and some calf manna and mix with baby food (fruits seem best, oddly enough) into a soft mush and get your animal to eat it. Weight loss is dangerous. If your chinchilla's weight drops below 14 ounces (400 Gm), your chinchilla is in danger of failure to thrive and needs to be fed frequently. Stay in close contact with your vet here, as this is probably a major problem.
