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Intermittent Soft Cecotropes in Rabbits

Date Published: 11/11/2009
Date Reviewed/Revised: 12/07/2009

Cause of Intermittent Soft Cecotropes (ISC)

*Please note that it will be helpful to the understanding of this disease if you first read the Care of Rabbits handout in order to understand the normal diet of the house rabbit. In addition you may wish to read the handout Hairballs in Rabbits for a more complete description of gastrointestinal tract function in the rabbit.

A common complaint of rabbit owners is having their pet produce normal dry stools along with soft, semi-liquid droppings that stick to the rabbit and to the surroundings. The condition can last for months or even years. Affected rabbits are often still bright, alert and eating well. The soft droppings stick to the rabbit's hindquarters, causing irritation and a foul odor. Defecation and urination can be hindered if there is sufficient buildup of feces. The soft stools range in consistency from a thick “pudding” to large semi-formed “blobs.” This material becomes smeared on the cage, carpeting and ultimately ends up caked on the bottom of the rabbit's feet. Despite these soft droppings, however, there is evidence of normal, dry, round stools being produced daily as well. Some owners observe that the soft droppings occur only at certain times of the day or night. This condition is the cause of numerous euthanasias and surrenders to shelters due to the high maintenance involved in cleaning the pet and the environment on a daily basis.  In a nutshell, the problem is not the production of soft stool (the waste material that makes up the round, dry droppings) but that the cecotropes, the nutrient-rich droppings produced by the cecum, are abnormally liquid and cannot be eaten.  We will refer to this condition as intermittent soft cecotropes (ISC) in this article.

It is important to differentiate this condition from true diarrhea. In true diarrhea (which is rare in rabbits), there is an absence of any formed stool and the consistency of the fecal material is watery. True diarrhea in a rabbit is a sign of a serious and often fatal condition. It is usually caused by an alteration in the flora (microorganisms) of the cecum, which is the fermentation area of the rabbit's gastrointestinal (GI) tract. Overgrowth of inappropriate bacteria such as Clostridium spp. or E. coli can result in the production of iota toxins. Iota toxins are absorbed into the bloodstream and produce a toxic condition commonly known as enterotoxemia. This condition can be fatal in 24 to 48 hours, particularly in recently weaned rabbits. Mucoid enteropathy is felt to be a less severe form of enterotoxemia seen in mature rabbits. In mucoid enteropathy there is production of clear mucous stools followed by gradual wasting, which if left untreated will lead to death. Clostridium spp. and E. coli bacteria are normally found in small amounts in the cecum and do not cause a problem. It is only when their populations grow abnormally that enterotoxemia occurs.

Some common causes for true diarrhea in a rabbit include:

  • Diet (overload of carbohydrates and/or insufficient indigestible fiber)
  • Inappropriate antibiotic use (many antibiotics are not safe for the rabbit’s GI tract)
  • Toxins from the environment such as heavy metal, toxic plants, etc.
  • Environmental stress
  • GI neoplasia (cancer)
  • Genetic predisposition
  • Severe metabolic disease (such as kidney or liver disease)
  • Infection with coccidia and/or rotavirus may contribute to the stress in the gut by causing mucosal damage but are not considered to be the major causes of diarrhea in rabbits.

    *The most common causes of true diarrhea in a pet rabbit are an inappropriate diet and inappropriate antibiotic use.

Diarrhea in rabbits differs from diarrhea seen in dogs, cats or humans. In rabbits the watery stools are caused initially by a decrease in intestinal motility and in dogs, cats and humans it is caused by an increase in motility. In rabbits, as the intestinal motility decreases, the material in the cecum is retained for excessively long periods of time, which then changes factors such cecal pH and volatile fatty acid production resulting in alterations in the flora. This is when Clostridium spp. and E. coli can overgrow, produce iota toxins and thus wreak havoc on the body.

In cases of ISC in rabbits, there is also an alteration of the flora in the cecum, but it is less severe than that seen with enterotoxemia. The soft stools are actually malformed cecotropes that should have been eaten directly from the anus by the rabbit. You will notice that the soft cecotropes have a strong odor and contain mucous like normal cecotropes. When the contents of the cecum are retained for longer than normal periods of time the cecotropes are eventually excreted in a more liquid state and it is impossible for the rabbit to eat them. The mucous in these soft or liquid cecotropes causes them to adhere firmly to any surface, making it difficult to clean the pet and its environment. Not only is the condition messy, but there is a concern that the rabbit may be missing vital nutrition if he cannot eat the cecotropes.

Cecotropes and waste droppings are produced in different areas of the intestinal tract and at different times. In ISC the production of waste droppings is unaffected and they are formed normally and appear in the toilet area mixed with the soft stools.

ISC is a sign of a problem and not the problem itself.  The most common cause of ISC is an inappropriate diet that is too high in carbohydrates and/or too low in indigestible fiber. Other, more uncommon causes of ISS include: partial intestinal obstruction particularly in the area of the junction of the cecum with the small and large intestine, internal abscesses, neoplasia (cancer) and other systemic disease that causes changes in the cecum, such as kidney or liver disease.

There is no specific test to diagnose the cause of ISC. The diagnosis is based primarily on clinical signs and history, most importantly the diet and any current use of antibiotics, and a physical examination. It may also be necessary to do additional testing such as blood tests, urinalysis, fecal examination or radiographs to rule out other non-diet related causes of ISS in some cases.  Each rabbit is an individual.  In my experience, the vast majority  patients with ISS have been fed a diet composed primarily of commercial pellets with little or no grass hay. This diet is much too high in carbohydrates and often low in indigestible fiber. In addition, many clients neglect to mention that they feed treat foods, such as crackers and cookies or commercial rabbit treats, because they are fed in small amounts and owners don't feel that these items are significant. Unfortunately, these treat foods are all loaded with carbohydrates and can be a large part of the problem, even in small amounts. The next most common cause is the use of inappropriate antibiotics that harm the flora in the rabbit’s cecum. During a physical examination, many rabbits with ISS are significantly overweight with obvious fecal staining of the hindquarters or feet. Your veterinarian may wish to obtain a stool sample for microscopic examination. Rarely, parasites such as coccidia are seen and can be easily treated, but they are not the primary problem. More commonly a microscopic examination of the stool will reveal large numbers of yeast organisms, which reflect the abnormal flora in the cecum. These organisms exist in small numbers in the normal cecum, but overgrow to large numbers when the environment of the cecum is abnormal. It is completely unnecessary to attempt to eradicate these yeast organisms because they will return to normal numbers when the ISS is treated with diet change.

Treatment of ISC

The treatment of uncomplicated ISC (meaning the cause is primarily an inappropriate diet) is based on converting the rabbit to a healthy diet that is high in indigestible fiber, which normalizes the motility of the GI tract and lower in carbohydrates, which helps normalize the flora in the cecum. A healthy diet for a house rabbit consists of unlimited grass hay as its primary component with additional green foods and limited high fiber/low energy pellets. This is not a difficult diet to feed, but it requires a commitment to removing high carbohydrate foods from the diet and never giving them again. If you do choose to slip some high carbohydrate treats to your pet from time to time, it is highly likely that the ISC will return within a short time and you will be cleaning the rabbit and cage all over again. The benefits of a healthy diet are not only getting rid of the ISC, but also improving your rabbit's dental, GI and mental health. Only you have control over the success of this treatment.

*NOTE:  Prior to treating your rabbit for ISC, it is advisable to have your veterinarian do a complete physical examination and perform any additional tests that might be needed as described above.

Treatment of ISC

The treatment of ISC is based first on a serious diet restriction to grass hay, which acts to return the GI tract to normal, and secondly a gradual reintroduction of additional foods after normal cecotropes are produced for at least a week.  This would mean you are no longer seeing the soft cecotropes in the environment or on the rabbit.  You will see the normal round, dry waste droppings and only the occasional formed cecotrope in the litter box or cage floor.

Part 1:  Improving the Diet with Dietary Restrictions

Grass Hay

For Rabbits already Eating Grass Hay
The most important part of the treatment of uncomplicated ISC is to feed grass hay to your pet. This should be the only food given until the stools return to normal. You must remove all other food items from the diet including pellets and treats. Provide the grass hay in unlimited amounts and have it available at all times to your pet. In this way your pet will never have to worry about going hungry and will have healthy food to eat.  Use several containers for the hay to encourage your pet's interest, such as hayracks, boxes or baskets. Avoid the use of legume hays such as alfalfa because they are much higher in carbohydrates and may not work as well to resolve the ISS problem. Appropriate grass hays include timothy, orchard, brome, oat and mixed grass.  It is preferable, if possible, to feed more than one type of grass hay for variety.  If this is not possible, any of the hays mentioned may be used. 

The return to normal stools may take two weeks to three months, depending on the severity of the disease in your pet. The hay acts to return normal motility to the GI tract and normal flora to the cecum eliminating the soft stools entirely. If you cheat and feed treats during this process, the treatment will not be effective and you will only perpetuate the problem. There is no doubt that your rabbit will not be happy with you for a while and will probably throw a few tantrums. After all, when you remove the pellets and treats from the diet, it is like taking chocolate away from a chocoholic! You need to resist your pet's attempts to manipulate your emotions and remember that this treatment is for her benefit and for your benefit as well when you have the freedom from cleaning up the mess every day!

Another important benefit of feeding the grass hay to the exclusion of other foods initially is that your pet will experience a healthy weight loss. Many rabbits with ISC are overweight, and not only do they feel sluggish because of the GI problems but because of their weight it is more difficult for them to exercise. Rabbits do not become underweight on this diet so you do not need to monitor the weight. Many of our clients comment that after the treatment for ISS their rabbit experienced a new “lease on life” and was as active as a young bunny again! It must feel good to shed the excess weight and to have normal GI function again!

NOTE:  How do you know your rabbit is eating enough hay?  You will know because the waste droppings (the round, dry droppings in the bottom of the cage) will continue in a large number and will stay a large size.  If these droppings decrease to half or less in size or greatly decrease in number or become greatly misshapen, then your rabbit is not eating enough and you need to check with your veterinarian to make sure there is not some other disease process going on.

For Rabbits not Currently Eating Grass Hay
Some rabbits have never had the opportunity to eat grass hay and they could starve if they are suddenly given grass hay and nothing else.  So we have to start more gradually and make adjustments in the pellets and introduce hay at the same time.

Go ahead and put grass hay in the cage and particularly the litter box area (no, they will not eat soiled hay so don’t worry, but many rabbits like to eat while they use the bathroom and this can help get them to eat hay).  Your rabbit might eat hay right away and your problem is solved.  For those that refuse we have more suggestions below, but the next step for these rabbits that refuse to eat grass hay is to get your pet on a healthy pellet and start reducing the amount.

First of all, you need to determine what’s in the pellets you are feeding.  Look on the label and note if it is based on based on grass hay (most often it will say timothy hay, but it can be any grass hay). This will be a healthier alternative to pellets with alfalfa hay as their main ingredient in the long run. Additionally if you are currently feeding a pellet mix that contains seeds and nuts you need to make the same switch to a grass hay pellet. Seeds and nuts add a lot of extra calories and starches and can be part of the problem. Start mixing the lower energy pellets with the pellets you are currently feeding about ½ and ½ for about one to two weeks to see if the rabbit cleans up the food.  Once that happens then go ahead and switch over to the grass hay based pellets entirely.  Rather then a full bowl of pellets in front of your rabbit all the time, try feeding in smaller amounts two to three times a day to monitor what he/she is actually eating. 

During this pellet conversion it is important to STOP ALL TREAT FOODS!  That’s right, ALL treat foods. For one thing, they are generally part of the problem and two, they will provide enough calories that your rabbit may not get hungry enough to have an incentive to change to a new pellet or to start eating hay.  SO NO TREATS!!! 

Now that your rabbit is eating healthy pellets reduce the amount of pellets to 1/4 cup per day for each 5 pounds of body weight. Divide this into a couple of feedings a day.  Keep giving them hay. Once the pet starts eating the hay gradually reduce the amount of pellets to zero over the next week and continue with feeding only grass hay as described in the section above until the soft stools are gone for a week.  Monitor the waste droppings as described above to make sure your pet is eating sufficient amounts of hay.

Rabbits that will only Eat Alfalfa Hay or Refuse any Hay
Some rabbits just don’t want to eat any hay.  There can be several reasons, such as the hay is old, moldy, too “stemmy” (not soft and grassy), it is put in an area that is not appealing to the rabbit and so on.  Below are a few tips for enticing your pet to eat grass hay:Alfalfa hay may be the only hay available in your area, or your pet may absolutely refuse to eat grass hay and will only eat alfalfa. It is better to feed some type of hay rather than no hay at all and you can continue with the same plan described for treating ISC with grass hay. However, be aware that some cases will never completely resolve due to the high carbohydrate content of the alfalfa hay. You can still add green foods to the diet as described below if the ISS shows considerable improvement.

  • Put the hay in the litter box - this is often the favorite place to eat hay!
  • Put hay in baskets or stuffed in empty toilet paper or paper towel rolls around the exercise area.
  • Try different types of hay.  There are several online hay sources where you can order small bags of different types of grass hay.  A different type may be more appealing.  Hay should be fresh smelling and not overly dusty.
  • Try pulverizing the pellets your are feeding in a blender or food processor, sprinkling some hay with some water and then dusting the pellets over the top to entice your bunny to try the hay.

Part 2:  Adding in Other Foods

Once the soft droppings have resolved for at least week, it is time to try adding in some additional foods.  Although technically a rabbit could survive on good quality mixed grass hay, it is likely that it will not be complete for the life of the rabbit and will be missing some trace nutrients.  In addition, rabbits are used to eating a wide variety of textures and tastes and it is much healthier mentally to have a variety of foods in their daily lives.  We need to add these foods back in carefully though, because your bunny has a history of GI unbalance and we don’t want to return to that state.  Remember that from here on out, your rabbit should ALWAYS have grass hay available as the basis of a good diet.

Green Foods
After your pet's cecotrops have returned to normal for at least a week, it is time to introduce green foods into the diet. These foods provide a variety of nutrients as well as moisture. We suggest adding one new green food every 48 hours to make sure no soft stools are being formed. You can easily determine which items are problematic if you only feed one green food every 48 hours, then remove the offending item if needed. Once you have tested several green foods, then you should feed at least three types daily to your pet  Feed a maximum of about  1 packed cup of green foods per 2 pounds of body weight at least once a day or this amount divided twice a day.

Examples of Green Foods  

Baby greens
Bok choy
Broccoli (leaves and top) 
Brussels sprouts 
Cabbage (red, green, Chinese) 
Carrot/beet tops 
Celery (leaves are good)
Collard greens  Dock 
Dandelion greens (and flower)
Leaf lettuce 
Mustard greens 
Parsley (Italian or flat leaf best) 
Romaine lettuce 
Swiss chard (any color) 
Water cress    

Healthy Treat Foods
When your rabbit returns to normal stool production and after the introduction of green foods you can try feeding small amounts of fruits and other vegetables as treats. As with the green foods, if you see any soft stools, remove the item from the diet. The maximum amount of a treat food is one tablespoon per two pounds body weight of any combination of the following:   

Bean or alfalfa sprouts 
Cactus fruit 
Edible flowers from the garden (organically grown and NOT from a florist) such as roses, nasturtiums, day lilies, pansies and snap dragons 
Green or red bell peppers 
Kiwi Fruit 
Pea pods (flat, NO peas) 

After introducing greens and fruits and vegetables back into the diet for two weeks without any relapse to soft cecotropes, then it is time to try pellets again.  It is important that you only use the grass-based pellets and not alfalfa-based pellets because you increase the likelihood of a problem with the high calorie alfalfa-based pellets.  You can try adding in about 1/8 cup per 4 lbs of body weight initially and go up to no more then ¼ cup of pellets per 4 lbs body weight per day maximum.  If the soft cecotropes return, remove the offending pellet and you may try a different brand of grass-based pellet.  If the soft cecotropes return no matter what brand you feed, then you may have a rabbit that simply cannot tolerate pellets.  In this case you can increase the consumption of greens to twice the amount listed above per day.  This happens in a small population of rabbits and if necessary they can live successfully on a free-choice grass hay and moderated greens/vegetable/fruit diet without pellets.

Forbidden Foods
Never again feed commercial rabbit treats or high carbohydrate snacks which include those found in the following list:   

Beans (of any kind) 
Refined sugar 
Any other grains

Your veterinarian may prescribe a vitamin supplement during the initial treatment for ISC, particularly if this has been a long-standing problem. If a rabbit cannot eat the cecotropes, then she may be missing vital nutrients those special droppings provide. Vitamin supplementation should be short term and need not continue once the pet is on a healthy diet and is producing normal cecotropes. Some veterinarians feel that giving vitamin C during the treatment of ISS is helpful in improving the integrity of the wall of the cecum and decreasing toxin absorption into the body. Most rabbits will readily take chewable vitamin C tablets, should they be prescribed. The dose is 100 mg per 5 pounds of body weight one to two times daily. Vitamin C should also be discontinued once the cecotropes return to normal.

Working with Your Veterinarian

It is important to keep any recommended recheck examinations and phone reports for your pet as suggested by your veterinarian. The progress of treatment can be evaluated and detection of any other diseases can be made. If the condition of ISC cannot be resolved with dietary treatment then your veterinarian will need to perform further diagnostic investigation to determine if there is additional disease. If you are having difficulties converting your rabbit to the diet suggestions made above, please consult your veterinarian and work with him or her so your rabbit can be monitored during this process.


ISC is most often caused by an inappropriate diet and in these cases it is not difficult to treat.  It does, however, require a commitment by you, the caregiver, to provide a healthy diet for your pet for the rest of the pet's life. It won't be easy at first as your pet becomes frustrated at the loss of the unhealthy but tasty treats, but the end result is a rabbit who is more active, more responsive and no longer needs high maintenance care. By successfully treating the common dietary cause of ISC, many rabbits can be saved from unnecessary euthanasia and the owners saved from unnecessary anguish.

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