True intermittent or chronic diarrhea in rabbits is the passage of unformed, loose, watery or runny fecal matter. True diarrhea should not be ignored or confused by the presence of uneaten caecotrophs as it is fatal – your pet can die in 24 to 48 hours.
This is a life-threatening condition that leads to dehydration that may cause sudden death. True diarrhea is often noted in baby rabbits or kits as opposed to older ones. . Young kits taken away from their mothers when they are not ready for weaning are the most common victims.
Cecotropes or fecal pellets?
Rabbits have two types of droppings. The fecal pellets that are dry, spherical and almost odorless with mainly undigestible fibers as well as cecotropes which are not feces, and often eaten from the anus (cecotrophy).
Cecotropes are “dark brown mulberry, or tightly bunched grapes”  with soft shiny and smaller elongated pellets coated with mucus. They have a pungent odor but are very nutritious and essential to rabbits.
Rabbit owners must understand the difference between these two types of droppings and not to confuse cecotropes for diarrhea.
Unformed cecotropes and cecal dysbiosis
Intermittent soft cecotropes or unformed cecotropes are often due to poorly formed cecotrophs caused by mainly cecal dysbiosis.
Cecal dysbiosis is due to a shift in the cecal flora where good bacteria such as Bacteroides spp. are outnumbered by harmful ones such as Clostridium spp. or fungus (yeasts) such as Saccharomycopsis sp.
Cecal dysbiosis often results in pasty, runny, liquid and mushy cecotrophs that often stick on a rabbit’s bottom (anal region) and have a foul smell.
Common causes of cecal dysbiosis and unformed cecotropes include a diet high in carbs and low in fiber, rapid diet change, excessive amounts of veggies (succulent foods) that have high water amounts, too many sugary treats, grains or some human foods among others.
Finally, partial obstruction especially at the cecum junction, antibiotic use, among others can cause intermittent soft cecotropes (ISC).
Rabbit baby diarrhea and weaning stress
Kits aged 3-4 weeks are susceptible to this problem during weaning as their digestive system may not be able to handle new foods. Weaning can cause enteritis that can cause diarrhea. This condition is fatal.
Let kits be with their mother until they are at least 8 weeks of age. Do not sell those less than this age as they still need their mother’s milk. Weaning will affect their GI tract pH as well as deprive then of antibodies in their mother’s milk. The milk makes their stomach sterile.
Most of the other factors we are going to discuss below will also affect kits unless they are unique to old rabbits.
Causes of diarrhea in rabbits
Causes range from infection to diet to antibiotic use. Here are some of the reasons why your rabbit may have a runny stomach.
Disease and infections
Various viral, protozoan, fungal or bacterial infections can cause diarrhea. Some of the common infections include:
- Cecal dysbiosis – This is the shift in the bacterial balance in the cecum characterized by having more of the harmful bacteria than the good ones. Cecotropes will be foul-smelling, clumpy, “mushy, pasty or even liquid.” 
- Rabbit Hemorrhagic Disease – This disease may be associated with diarrhea or sometimes constipation.
- Enteritis -The inflammation of the gastrointestinal tract. This may include mucoid enteropathy as well as enterotoxemia.
- Escherichia coli infection –A bacterial infection which can be transmitted even by handlers and known to cause diarrhea among other symptoms
- Tyzzer’s disease – caused by Clostridium piliforme signaled by watery diarrhea, depression, a ruff coat, emaciation, lethargy, hypothermia among other signs.
- Viruses – Viruses such as Coronaviruses and Rotaviruses have been associated with diarrhea.
Abrupt diet changes, giving your pet wrong foods such as lots of grains, fruits, crackers, bread, sweets, and foods that have low fiber and high carbs can trigger various conditions that lead to diarrhea. For instance, “anorexia and diarrhea after consumption of a large amount of unfamiliar green food”  are possible.
Runny cecotropes are possible in case of diets that have high amounts of digestible carbs. Also, little fiber will cause diarrhea.
Various intestinal parasites have also been associated with diarrhea in both young and adult rabbits. Some of these parasites include:
- Coccidiosis – A protozoal infection that is highly contagious caused by Eimeria protozoa species with 12 species of this protozoa already found to affect rabbits. Besides diarrhea, you may also note a mucous membrane that is pale.
- Roundworms and tapeworms
Obesity in rabbits makes them unable to reach their anus to consume cecotropes which are essential in balancing the gut as well as providing nutrition including some vitamins.
If your pet does not get the healthy organisms found in cecotrophs, there may be an imbalance in the cecal flora and possibly overgrowth of the harmful bacteria.
It causes similar problems as obesity especially if it affects the hip and spine. They cannot reach their cecotropes and will be inactive.
Inappropriate drug use
Some medicines, especially antibiotics may wipe the good bacteria inside the gut leading to an imbalance that may bolster harmful microorganism overgrowth that may cause diarrhea among other gastrointestinal health problems.
- Ingestion of toxins such as heavy metal or toxic plants
- Stress associated with the change of environment, scare from predators, noise, heat stress, and so on. Stress affects their eating behaviors
- Metabolic disorders such as kidney or liver diseases
Other problems including urinary tract disorders, head tilt, dental problems, upper respiratory infections may cause pain and stress thereby affect normal intestinal emptying such resulting in problems GI stasis and diarrhea. 
The obvious symptom is the presence of unformed, loose or watery feces that may contain mucus or not. Other possible symptoms to be looking for include the following:
- Anorexia (reduced appetite) and your rabbit unwillingness to eat which may cause weight loss
- Poopy butt – feces stuck on the rabbit’s bottom, this could encourage flystrike
- Inactivity due to diminishing quality of life
- Stomach rumbling or other gas in rabbit signs
- Extreme thirst indicated by it looking for water or spending more time drinking water
- Their belly including cecum may be filled with fluids that make a sloshing sound due to the much fluid accumulation.
- Hindquarters of your rabbit may look sore, raw or black fur.
- Abdominal discomfort indicated by hunched or stretched posture or teeth grinding.
There may be other symptoms that may be specific to the underlying cause. Different causes may have slightly different symptoms.
Diagnosis will involve examination of cecotrophs and fecal pellets (grams staining, direct smear flotations), and test for various infections as well as for the presence of parasites.
Therefore, expect blood tests, urinalysis, radiographs, abdominal ultrasounds, Pasteurella tests, serum chemistry, among others.
Treatment and prevention
If you notice some of the signs we have mentioned, inform your vet immediately. Treatment options will be influenced by the cause of diarrhea and severity. Treatments will involve treating any underlying condition as well as adopting preventive measures. This will include:
They are fashioned to deal with the underlying cause which may include parasites, bacteria, protozoa among other microorganisms responsible for diarrhea, reducing pain and dehydration. Some of the treatments your rabbit savvy vet may prescribe include:
- Antibiotics including metronidazole and ciprofloxacin. Oral ciprofloxacin will work faster compared to the injected one.
- Pain medications such as simethicone (gas relief), sulfasalazine, barium suspension (helps to stop diarrhea) and meloxicam.
- Anti-inflammatory medications or NSAIDs such as Banamine, tramadol. Banamine might require you use an antacid such as famotidine
- Anticoccidial medication i.e., coccidia parasites may be treated by ponazuril (most effective), sulfadimethoxine, bacterium or Trimethoprim Sulfa.
- Subcutaneous injections with fluids such as Lactated Ringers Solution to help it keep hydrated and retain the normal electrolyte balance.
- Helminthicidal medications such as Panacur to kill intestinal parasites such as tapeworm, or nematodes.
- In case of arthritis, your vet may prescribe NSAIDs, Cetyl-M or myristoyl glucosamine supplements to help deal pain.
Prevention and managing diarrhea
Besides the above treatments, here are more ways to manage diarrhea as well as prevent it from occurring.
- Do not starve them. Unlike in carnivorous animals, you should not fast your bunnies while they are having diarrhea.
- Opt for grassy hay during weaning. Also, weaning should be down slowly to give the kit time to adapt to the new food you are giving it.
- Avoid weaning kits early. They need their mother’s milk which has strong antibodies and will help keep the right gut pH. Let them, nurse, until they are at least 8 weeks old.
- Ensure the proper sanitation and avoid overcrowding as these two factors could cause infections and make the contagious ones spread easily.
- Manage obesity by encouraging your rabbit to exercise, going for high fiber – low-calorie foods such as timothy hay. Reduce commercial pellets, starchy treats among other strategies.
- Provide unlimited grassy hay using hayracks, baskets or boxes. High fiber diets, preferably grassy hay such as timothy, oats, wheat or brome will help restore the gut floral balance fast. Alfalfa and other legume are not recommended as they are higher in carbs and proteins unless they more protein need. Hay helps boost peristalsis which promotes food movement, weight loss, healthy teeth among other benefits.
- Introduce new diets gradually and mixing with the old ones. Do not change their diets in less than 7 days.
- Spot clean soiled bottoms using a damp towel or piece of cloth but for hardened feces, you might have to give it a shallow bath with warm water in only submerging the affect areas to reduce stress. Use animal shampoos not humans as you wash it.
- Help old, arthritis or those suffering from any condition that affects their mobility to groom. This will reduce the chances of flystrike.
Rabbit diarrhea but still eating
If your rabbit has diarrhea but still eating, you should still consider treating the underlying cause as well as modifying its diet to include unlimited amounts of grassy hay. This will help it regain fast. You should feel lucky if your rabbit has diarrhea but still eats.
Do not forget that the threat of dehydration still exists. Provide unlimited clean, fresh water to help in rehydration and notify your vet if it persists for more than 12 hours.
Rabbit Diarrhea not eating
Diarrhea without eating and drinking will cause weight loss, malnutrition, shock, and death. Your vet should consider forced feedings such as using products from various manufacturers including Oxbow, Burgess, Lafeber, and Supreme
Check if the food you are offering is fine. It may be moldy, old, and not appealing to your pet.
Also, try changing their diet and give them something more appealing to see if they just do not like the food you are offering.
Finally, consider foods that will boost their appetite.