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The intestine picks up where the stomach leaves off, and it does most of the actual work of digestion. The small intestine, made up of the duodenum, jejunum, and ileum, is where enzymes finish breaking food down and where the bulk of nutrient and water absorption happens across a lining folded into millions of tiny finger-like villi. The large intestine, including the cecum, colon, and rectum, reclaims remaining water and hosts a dense population of bacteria that ferment fiber and other undigested material.

This bacterial population, often called the gut microbiome, plays a genuine role in digestion, in supporting the immune system, and in keeping harmful organisms from gaining a foothold. Because the intestine is so long and does so much, disease here can show up as anything from mild, self-resolving loose stool to severe, whole-body illness. Species differences are significant too: some animals depend heavily on their large intestine for fermenting fiber, while others use it mainly to concentrate stool before elimination.

The small intestine has three sections. The duodenum receives partly digested food from the stomach along with bile and pancreatic secretions, the jejunum is the longest section and does most of the nutrient absorption, and the ileum absorbs what remains before handing material off to the large intestine at the ileocecal junction. The lining throughout is covered in villi, tiny projections that dramatically increase the surface area available for absorption.

The large intestine varies more by species than almost any other digestive structure. Horses and rabbits are hindgut fermenters with an enormous cecum that ferments plant fiber the small intestine could not break down, a process that can take a full day or more. Cattle, sheep, and goats already ferment fiber earlier in the rumen, so their intestine focuses mainly on absorption rather than further fermentation. Birds have a shorter intestine overall along with a pair of ceca, and dogs and cats, as carnivores, have a comparatively short, simple intestinal tract suited to a diet lower in fiber.

Enteritis, inflammation of the intestine, has many possible causes: viral infections such as parvovirus, bacterial infections, and parasites including roundworms, hookworms, whipworms, and coccidia, all common enough to warrant routine screening in most companion animals. Chronic enteropathies, sometimes labeled inflammatory bowel disease, cause recurring diarrhea or weight loss over months and often respond to changes in diet alongside other treatment.

Physical problems occur too. Intussusception, where one segment of intestine telescopes into an adjoining segment, can follow a bout of severe diarrhea, particularly in young animals, and typically requires surgery. Foreign objects that pass the stomach can still lodge further along the intestine and cause a full obstruction. Colitis, inflammation specifically of the large intestine, causes frequent, small amounts of stool with straining and sometimes mucus or blood. Rabbits and horses can develop impactions in the cecum or colon, often linked to inadequate fiber intake or dehydration, and these range from mild to genuinely life-threatening.

Diarrhea from the small intestine tends to be larger in volume and less frequent, sometimes with a change in color, while diarrhea from the large intestine is typically smaller in volume, more frequent, and more likely to include straining, mucus, or fresh blood. Recognizing which pattern you are seeing helps your vet narrow down the likely cause even before any testing, since the two patterns point toward different segments of the tract.

Beyond stool changes, watch for excess gas or a bloated appearance, weight loss despite a normal or increased appetite, a sign of poor absorption, and general lethargy in more chronic cases. A rabbit or horse that stops producing droppings or manure entirely is showing a red flag rather than a minor symptom, since gut motility in these species needs to keep moving fairly constantly. Straining repeatedly with little or nothing to show for it, in any species, points toward either severe inflammation or a physical blockage, and it is worth noting how long the straining has been going on when you describe it to your vet.

A single episode of soft stool in a pet that is otherwise bright, eating normally, and playful is reasonable to watch for a day before calling the vet. Many mild cases resolve once whatever triggered them, a new treat, a stressful event, a minor dietary indiscretion, clears the system on its own, without any need for medication or a clinic visit.

Schedule a same-day visit if diarrhea continues past two days, if you see blood or mucus, if straining occurs without much result, or if the pet is losing weight. Treat it as an emergency if bloody diarrhea appears alongside lethargy or vomiting in a young or unvaccinated animal, if signs of dehydration develop such as tacky gums or skin that stays tented when gently lifted, or if a pet, rabbit, or horse stops passing any stool at all while straining, which can indicate a complete obstruction needing urgent surgical care rather than a wait-and-see approach at home.

What's the difference between small and large intestine diarrhea?

Small intestine diarrhea is usually larger in volume, less frequent, and may include weight loss from poor nutrient absorption. Large intestine diarrhea tends to happen more often, in smaller amounts, with more straining and sometimes visible mucus or blood, since the large intestine handles final water absorption and stool formation.

Are intestinal worms common in pets?

Yes, intestinal parasites such as roundworms and hookworms are common enough in dogs and cats that routine deworming and fecal screening are standard parts of preventive care. Many infected animals show mild or no obvious signs at first, which is part of why routine screening matters.

Can changing my pet's food cause diarrhea?

A sudden diet change is one of the most common causes of short-term diarrhea, since the gut's bacterial population needs time to adjust to new ingredients. Transitioning to a new food gradually over a week or so, mixing increasing amounts of the new diet with the old, usually prevents this.

Why is my rabbit not passing droppings?

A rabbit that stops producing droppings may have gut stasis, a serious slowdown or stoppage of normal intestinal movement that can happen quickly, often linked to inadequate fiber, dehydration, pain, or stress. This needs same-day veterinary attention rather than a wait-and-see approach, since rabbits can decline rapidly once the gut stops moving.

When is diarrhea serious enough for an emergency vet visit?

Treat it as an emergency when diarrhea is bloody and paired with lethargy or vomiting, especially in a young or unvaccinated animal, or when there are signs of dehydration such as sunken eyes or gums that feel tacky rather than moist. A pet straining repeatedly and producing nothing at all also needs urgent evaluation.