Why Does My Rabbit Poop in His Hay?

Surely your rabbit loves hay just as much as the next rabbit. In fact hay makes up eighty percent of the animal’s diet. But perhaps you’ve noticed your furry friend has been leaving droppings in its favorite snack. Depending on the cause, there is most likely no reason to worry, however this issue may never resolve entirely.

So, why does my rabbit poop in his hay? The main reason is that rabbits love to munch on hay while they take care of their business and because of this some droppings will end up in their hay in the process. However, there are ways to set up your rabbit’s hatch to keep their hay clean.

First we’ll detail how to set up your pet’s habitat with a litter box. Then we’ll talk about other reasons to explain why you’re finding droppings in your rabbit’s hay and the steps you can take towards a solution. We’ll show you what to look for when observing your rabbit’s excrements and finally a general good diet for rabbits. 

Litter Box Setup

Rabbit in its wooden litter box
Rabbit in its wooden litter box | image by Alexas Fotos via Pexels

Setting this up is fairly easy. All you’ll need is what follows: 

  • Shallow storage container 
  • Recycled paper litter 
  • Hay
  • Feeder, hay rack, or separate small box 

If you have a shallow storage container, you’re already halfway to having a litter box for your rabbit. The next step would be to fill it with a layer of recycled paper litter. Don’t worry about filling the container up, just a thin layer is good enough since rabbits leave their droppings rather than burying them.

And to top it off, include hay either directly in the litter box or in a box outside of it. You could even put in a feeder or hay rack above the box. Regardless, everything should be positioned in a way that allows your rabbit to sit in the litter box and still have access to the hay. This way the droppings can end up where they are supposed to go. 

It is imperative to have hay available to your rabbit at all times because rabbits require high amounts of fiber in their diet and hay is a great source of it. In general, hay will help regulate the digestive tract. 

As your rabbit learns to excrete in the litter box, it will of course make mistakes. No one’s perfect! When this happens, to teach your rabbit, just pick up its droppings and put it in the litter box. If this does not work, you definitely have a stubborn bunny on your hands. At that point, if your pet prefers a certain area to poop in, you might have to concede and move the litter box there.

On the other hand, if your rabbit is pooping pretty much everywhere, it could be a sign of them marking their territory. In that scenario, it would be best to discuss the option of neutering with your veterinarian. 

General Habitat Setup 

In regards to the general setup of your rabbit’s habitat, or hutch, there should of course be a separate area for sleep, exercise, and the litter box. To have a cramped habitat would only increase the chance that droppings get in the hay. 

Lastly, to maintain cleanliness, sanitize the hutch around three to four times a week.

Is There Just Too Much Poop?

Rabbit with hay
Rabbit with hay

There certainly could be other reasons as to why you are seeing droppings in your rabbit’s hay. One overarching reason is because perhaps there are just too many excrements in general. There are a multitude of causes that would explain excess droppings which can come in the form of cecal dysbiosis or diarrhea

Cecal Dysbiosis

Cecal dysbiosis is a type of unformed rabbit dropping. The culprit is unbalanced gut bacteria and it can also be a symptom of an underlying illness. The smell will be pungent and can adhere itself to your pet’s bottom and will collect there over time. 

A high sugar, low fiber diet can absolutely cause and exacerbate cecal dysbiosis. This is where something like hay can help immensely as it is a huge part of the rabbit’s diet and has fiber.

You definitely won’t have trouble getting your rabbit to chow down on some timothy hay. Be sure to mix up the type of hay you are feeding your friend, make life a little more interesting! Your best bet is to go with a type of grass hay. 


Now, diarrhea is rare, but if you notice it you need to take your rabbit to the vet as soon as possible. There could be a parasite or some type of poison in your animal’s system. Both diarrhea and cecal dysbiosis will be mushy and if seen, should be addressed immediately. 

Abnormal Poop

White rabbit on hay
White rabbit on hay | Image by Hans Benn from Pixabay

If you are noticing that after being trained, your rabbit is starting to poop everywhere again, or they are straying from their normal habits, it could be a sign of an underlying illness. You can study their droppings which could  point to the specific problem and below we will tell you what to look for.

Normal Poop 

To know what abnormal poop is, you need to know what to compare it to. The physical appearance of normal rabbit poop will vary based on the individual rabbit. The size of the poop may not even align with the size of the rabbit.

So to see if your rabbit’s poop is normal look for uniformity. All droppings coming from one rabbit should be one size. A rabbit’s excrements should also be hard, not mushy, and with minimal smell. 

Now that we know what normal rabbit poop is, we can look at what is abnormal. 


Cecotropes are actually perfectly normal rabbit droppings, but they might look odd to you if you are not used to seeing them. There is a chance you have never seen one of these because most of the time your rabbit will eat it as it is packed with nutrients. 

These droppings are usually in groups or clusters, almost like grapes and not unlike grapes, they are soft and squishy. Their sticky texture can also cause hay or fur to stick to it which could be why you are finding them in the hay. 

Copious amounts of cecotropes most likely means your rabbit has been consuming too much sugar. Just give your rabbit what it wants: hay, hay, and more hay! 

Small Poop

If there are lots of small droppings in the hay, this points to emotional distress in your rabbit. Something in the environment could be alarming your pet and this is an inevitable occurrence. You definitely can’t control when a siren blares. Therefore, it is important to keep an eye on the pattern of droppings.

If small poop only appears for a short amount of time and then returns to normal then most likely it was just an event that caused them to be stressed. If they are continuing their normal eating habits as well, they are most definitely okay. But if the poop does not return to normal, then it is time to take your rabbit to the vet and get a professional opinion. 

Double Poop

Double poops are when it looks like two normal poops have been merged. Seeing double poops for a short amount of time (just a few per day) is normal. It occurs when the rabbit’s digestive tract slows down because it was startled.

Just like with small poops, the appearance of double poops are inevitable, but if it persists your rabbit should be taken to the vet to see what options there are to normalize the gut speed. While there are various other kinds of abnormal poop, most abnormalities can be attributed to an unbalanced diet. 

Proper Diet

In general, a rabbits diet must include copious amounts of fiber. Fiber can help maintain gut and also teeth health. Hay should always be present in their habitat, and as discussed before, it is ideal to keep it near their litter box so they can eat and excrete, just the way these fluffy creatures like it.

In addition to fiber, fresh vegetables are an ideal part of the diet. About two cups a day is more than enough. It is important to research what foods are best and what foods are toxic for your rabbit as is this just a brief description of what the diet should be. 


Finding droppings in the hay can be a nuisance, but there is no need to worry. You might feel that hay is being wasted and we described ways to help prevent that. One way being to put the hay in or near the litter box.

If there is more poop present in general, you can observe the droppings and attempt to pinpoint the issue. The reason behind many abnormalities in a rabbit’s poop is an unbalanced diet so ensure lots of fiber and minimal sugar in the diet. 

At the end of the day, finding poop in your rabbit’s hay is not unusual and there is not one tried and true solution for it. As long as you are ensuring a clean, comfortable environment and a proper diet, your rabbit is surely happy. 

After all this, it’s clear, the way to your rabbit’s heart is through its stomach.