Pet Factsheets

Dirty bottom syndrome

There are a variety of reasons why rabbits may suffer with a dirty bottom, either with faeces or urine, both of which are potential attractions for flies, especially in warmer months of the year when flystrike is a common occurrence. Having urine or faeces around their bottom can also cause the skin to become sore, inflamed and infected, so it is important to understand why the rabbit is affected and what can be done to resolve the problem.

What causes dirty bottom syndrome?

If your rabbit is suffering from a dirty bottom it is imperative to find the cause and treat the underlying problem, to ensure that your rabbit is clean, happy and comfortable, and aren't an attraction for flies.

The following are some of the most common reasons for a rabbit to suffer from a dirty bottom.


Rabbits who are fed too many pellets, are fed muesli-based concentrates and don't eat enough hay, or are too full to eat their caecotrophs, are likely to get a mucky bottom from the uneaten caecotrophs as they build up around their bottom. These rabbits also produce too many cecotrophs so although you may observe some caecotrophs being eaten, they won't be eating all of them like they should do.

Feeding too many greens has often been cited as a cause of diarrhoea in rabbits. It may be a cause of true diarrhoea (liquid faeces) but feeding greens doesn't cause the production of too many caecotrophs. All vegetables should be introduced slowly to avoid digestive upsets, but once you have done this, feeding greens causes the vast majority of rabbits no problems and is an enjoyable part of their diet.

A rabbit's diet should consist of a small amount (a maximum of 1 level tablespoon of pellets per kg of ideal bodyweight) of a good quality extruded nugget food (to prevent selective feeding), unlimited amounts of fresh grass and hay and a mound of fresh vegetables the size of their own body each day. This can be made up of herbs (parsley, mint, basil, coriander, etc), greens (spring greens, spinach, kale), broccoli, celery and naturally foraged safe plants (dandelions, etc).


An awful lot of pet rabbits are overweight to some degree, and many owners are not aware of this. If a rabbit can't physically reach its back end to clean itself or eat the caecotrophs as they are produced from the anus, then they will build up around the rabbit's bottom. Overweight rabbits often have an enlarged dewlap (fat pad under their chin) or a fat pad around their abdomen preventing them from reaching their back end. 

Losing weight is the only answer, but no rabbit should ever be put on a crash diet as rabbits must have a constant supply of food going through their digestive system at all times otherwise they will go in to gastrointestinal stasis, which can be rapidly fatal. Never be tempted to deprive your rabbit of food even for a short while. 

Instead cutting down on the amount of concentrated rabbit food that the rabbit is given and increasing the amount of hay and greens they eat, whilst also increasing the amount of exercise they do, should see them losing weight at a steady and slow rate, and being able to keep themselves clean.

Try scatter-feeding the pellet allowance to encourage the rabbit to forage and move around, hide pieces of fresh food for the same purpose. Make sure the rabbit has a companion to play with and toys such as tunnels and boxes to keep them entertained. 

Dental disease

Rabbits who find it painful to clean themselves or eat their caecotrophs due to dental disease will often present with a dirty back end, as well as the classic symptoms such as excessive salivation, loss/lack of appetite and weight loss.

The rabbit should have a thorough dental examination, under sedation or general anesthesia (after stabilisation if they are not eating/drinking), which should also include skull x-rays to assess the tooth roots. If the rabbit isn't well enough to undergo an anaesthetic immediately then supportive treatment in the way of syringe/tube feeding, intravenous fluid therapy, analgesia (pain relief) and prokinetic medication (to encourage the digestive system to keep moving) should be implemented until the rabbit is deemed fit enough to cope with an anaesthetic.

If dental disease is found to be the cause of the rabbit's dirty bottom, this is likely to be a lifelong problem as the rabbit's teeth will continue to grow throughout its life.

Strict preventative treatment for flystrike should be implemented, especially during spring, summer and autumn months of the year, which should include checking the rabbits back end 2 or 3 times daily, cleaning it straight away if it is dirty and using a product such as Rearguard or F10 for extra protection.

Arthritis / spinal problems

Large, overweight and senior rabbits are commonly affected by arthritic and spinal conditions, such as spondylosis. Such conditions often go under-diagnosed in rabbits as they tend to hide signs of weakness and pain due to their prey species instinct.

X-rays can detect problems and non-steroidal anti-inflammatory medications (NSAIDs) often help to ease the rabbit's discomfort and improve the clinical symptoms.

Changes may be required to the housing especially if the rabbit struggles with any ramps, etc or getting in and out of the litter tray. Low sided trays or those with a lip cut out should make this easier for them.


Those rabbits that are physically unable to get away from their droppings and urine as their housing is too small, have no option but to sit in it. Equally, those who are not cleaned out frequently enough will not be able to get away from sitting in urine and faeces. Litter trays should be changed daily.

Ensure that your rabbit has access to a run or enclosed and predator-proof garden all the time. Your rabbit should also have access to enclosed housing; this must be big enough (minimum of 6ft x 2ft x 2ft for the average sized pet rabbit), so they can use one corner as a toilet corner and have the rest of the hutch as a clean and dry area to sleep, rest and eat in. The full size of the enclosure should be at least 10ft x 6ft and allow 60 square feet for the rabbits.

Rabbits should not be shut up in hutches for any length of time.


Rabbits suffering from stones or sludge in their urinary tract (kidneys, ureters bladder or urethra) often have urine scalding/staining as a symptom. This makes them constantly wet, sore and very smelly.

To diagnose a problem often x-rays will often be needed. If stones are detected, then surgery may be an option to remove them and sludge may need to be flushed from the bladder under heavy sedation or general anaesthesia.

Many rabbits can be found to have a degree of sludge in their bladder and show no clinical symptoms, but if the rabbit has no other diagnosis then sludge may be the cause of their problems.

A change in diet to reduce the amount of calcium that the rabbit consumes and increase the amount of water in the diet should be implemented; your vet may also recommend surgery to flush the bladder and remove stones. Added to this, the vast majority of rabbits with sludge in their bladder are also overweight and inactive, and may also have osteoarthritis, so do not empty their bladder frequently enough or are not able to get into the correct position to urinate. These rabbits need a weight loss programme implementing and may benefit from medication if osteoarthritis is suspected.

Encephalitozoon cuniculi

E. cuniculi is a protozoal fungus. The fungus primarily affects rabbits, but cases have been reported in sheep, goats, dogs, cats, monkeys, guinea pigs, foxes, pigs and humans. It is a recognised zoonosis (can be transmitted to humans), but the zoonotic risk seems to be minimal to healthy individuals observing basic hygiene.

Urinary incontinence and scalding are a common clinical sign with rabbits suffering from an active E. cuniculi infection.

A blood test can determine if the rabbit has an infection that may be causing the clinical signs.

Often rabbits are treated without a definite diagnosis on clinical symptoms alone, using fenbendazole (Panacur) for 28 consecutive days and assessing the patient's response.

Often the rabbit will suffer from recurrent flare-ups during stressful occurrences and treatment will need to be repeated.

Should I clean my rabbit at home?

It is important that your rabbit is clean otherwise they are much more likely to get flystrike. Check your rabbit at least twice daily and if they are dirty should be cleaned. Never be tempted to bath your rabbit and never try to cut fur or faeces off with scissors; rabbit skin is extremely delicate and tears and cuts very easily, even if you are being very careful.

You will need someone else to either hold your rabbit or to do the cleaning. One person gently turns the rabbit so they are sitting on their bottom with all 4 feet off the ground. Do not turn the rabbit onto their back as this puts them in a fear, trance state. With some cotton wool, wet with warm water, you can gently clean the faeces or urine off the fur. Only wet the area you need to and be careful the rabbit does not become stressed or cold. If they dislike the procedure, stop and give them a few minutes break.

After you have finished cleaning them, carefully dry them with a soft towel. Be careful as the skin may be sore. Speak to your vet about applying a barrier cream if this is the case. If you get to the route of the problem, you shouldn’t need to clean your rabbit once this has been identified and addressed.

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