Rabbits often get diarrhea (called cecal dysbiosis) from eating an unbalanced diet that has too much starch (grain and grain-byproducts) and/or soybean meal. For the same reasons you should not feed your bunny treats that are high in sugar or carbohydrates because it will cause rabbits to have gas and bloat.
The diagram of the rabbit digestive tract at the bottom of the page explains in more scientific detail what actually causes diarrhea in rabbits.
Most rabbit pellets on the market contribute to rabbits contracting diarrhea because they have too much grain and not enough fat and fiber. This is why rabbit pellets have such a bad name. However, properly formulated pellets are a lot healthier for rabbits because they ensure your rabbits won't be deficient in specific vitamins and minerals that your rabbit needs. Although feeding rabbits extra hay is a quick fix to rabbit diarrhea, eating just hay and veggies will likely cause long-term degenerative health problems.
After the food a rabbit consumes passes through the stomach it travels down the small intestine where nutrients are absorbed. All nutrients should be absorbed by the time the food reaches the end of the small intestine (ileum). At this point the food particles that are not digested are sorted based upon size. The small particles (less than 1.7mm) move into the caecum (highlighted in yellow) for fermentation by good bacteria while the large particles move into the large intestine where water is absorbed before they are excreted as rabbit poop.
Diarrhea in rabbits is caused by undigested starch and protein supplements like soybean meal that enter into the caecum disrupting the normal fermentation process, changing the pH of the caecum, and favoring bad bacterial growth. Take note that certain strains of bacteria that are known to cause rabbit diarrhea are only a problem because they make the rabbit more sensitive when the rabbit is consuming a poor quality diet.
Baby rabbits require a high fat diet "like mamma's milk" that is also high in fiber and rich in specific nutrients needed to support healthy growth. The chart below compares the ideal baby rabbit food with other brands of rabbit food. Notice the starch and fat content of both styles of feed as well as the sources or ingredients used to make the feed.
Adult pet rabbits will be healthiest when fed a low-energy grain and soy-free rabbit food that is rich in grass hay like timothy hay. Also notice the starch, fat, and fiber contents of the ideal pet rabbit food below compared with most other pet rabbit food brands. DO NOT FEED TREATS... or at least keep them to a minimum. Feeding treats to your rabbit will upset this delicate balance and will dilute the nutrients they get in their diet. Hay is a great source of fiber but it is deficient in choline, phosphorous, and many key minerals.
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