Rabbits have a very clever gastrointestinal tract to help them extract nutrients from their diet; which should be predominantly 85+% hay and grass and 10%+ good quality leafy greens and only a small amount of good quality pellets. But it can go wrong sometimes, leaving them with a mucky back end…

Rabbit digestion (a quick overview)

When rabbits eat hay or grass, they chew thoroughly (very important for their dental health too) before swallowing, after travelling through the upper digestive tract it goes to the lower digestive tract, to the colon and caecum. This is where the fermentation occurs.

The colon of the rabbit separates the ingested food into two parts; a part that can be digested and the nutrients used by your rabbit, and the other indigestible part. The digestible part is sent to the caecum, where it’s mixed up with healthy digestive bacteria. It is kept in this organ for at least 4 hours for fermentation to occur. During this time the bacteria break the useful parts of grass/hay down and release the nutrients.

It is then coated in a mucus package and defecated as caecotrophs (also known as “caecals”) – however, it should be re-eaten by the rabbit! The mucus protects it from the very strong stomach acid for a few more hours to allow more nutrient production by bacteria fermentation, before the mucus is dissolved and the nutrients are absorbed in the stomach and small intestines. The indigestible part of ingested grass or hay is also important to help move the gut along and come out as faecal pellets; these pellets are usually round and crunchy!

If your rabbit has runny poo, this is very worrying and you should always act promptly to seek veterinary care. Rabbits are prey species (they are the hunted in the wild) and as such hide their illness until they are VERY poorly to avoid predation. It is better to act quickly if you notice runny poo in your rabbit.

Caecal Dysbiosis 

Caecal dysbiosis can occur for a number of reasons but sometimes in rabbits fed carbohydrate-rich diets. Affected rabbits intermittently pass thick, pasty stool with a pungent odour. Although this is not runny poo it can lead to enteritis which can cause runny poos.


Many cases of enteritis are secondary to caecal dysbiosis. It can occur in any age of rabbit but true diarrhoea in young rabbits may be the result of parasitic enteritis, usually secondary to Eimeria (coccidia parasites).

The bacteria Clostridium spiroforme and Escherichia coli are often key players

E. coli are present in low numbers in the cecum of every healthy rabbit. If something occurs to change this balance these bacteria get an opportunity to multiply to excess, then enteritis can occur. The most severe form of enteritis is associated with the multiplication of Clostridia and the subsequent production of iotatoxins, which leads to diarrhoea, dehydration and death.

Caecotrophs (caecals)

Caecals are not ‘runny’ but are certainly much softer than you will be used to seeing from your rabbits; they are soft, shiny and smelly and look like small beads all joined together and covered with a slimy coating.  These are entirely normal and your rabbit should eat them straight from his bottom as he produces them.

However, if you are seeing them regularly this needs investigation. You may think that your rabbit has soft stools when in fact they might just not be ingesting their caecals from their bottom. There are a number of reasons your rabbit might not perform caecotrophy (ingesting their caecotrophs); are they arthritic and can’t bend? Are they being fed foods that are too rich?  Or are they lethargic and too unwell to reach round? Are they obese and cannot bend enough to get them?

Word of warning

As said before, runny poos, whether excessive ceacals or true diarrhoea, require veterinary attention. Not only will your rabbit likely be poorly in some way but you also run the risk of fly strike which can also be life threatening.

What is flystrike?

Myiasis, known as flystrike, is mainly seen in the warmer months. It is a preventable condition but one that can quickly become life threatening if not noticed quickly.

Flystrike refers to damage done to skin when fly eggs are laid on its surface. These eggs hatch and become maggots which rapidly begin to feed on your rabbit’s (usually compromised) flesh.

It is important to remember that normal dry, clean skin that is free of caecotrophs will not attract flies. Therefore, if this occurs there is likely to be an underlying disease affecting the rabbit. This includes if they have diarrhoea or not eating their caecals – causing faecal matter to stick to their rear end.

The bottom line (excuse the pun)

The bottom line is that we need to take runny poos seriously, if you notice them act quickly to get them booked in with a rabbit savvy vet.

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