How to Keep Your Rabbit Enclosure Clean and Smelling Good


A step by step guide to clean your rabbit's space

As part of my work at the rescue center, I am responsible for cleaning out all of the rabbit and small animal enclosures. Since there are often a couple of handfuls of hutches that need cleaning, I’ve developed a streamlined approach to deep cleaning a rabbit enclosure.

On average, you should deep clean your rabbit’s enclosure about once every other week. The frequency will vary depending on your rabbit’s cleanliness and the type of enclosure you use. Specific tasks, such as cleaning the litter box, should be tackled daily to avoid a build-up of smell.

I’ve separated my cleaning routines into three categories: the ex-pen, the covered cage, and the cage with a removable top. The cleaning tasks are generally the same for all three, but the approach is slightly different, so feel free to skip to the section with the type of enclosure you use.


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Daily cleaning tasks for all enclosure types

Regardless of the type of enclosure you have for your rabbit, some simple daily tasks will make it much easier to keep a clean home. These tasks will also limit any smell from building up in your rabbit’s area, and they can prevent potential insect infestations.

The daily cleaning tasks include:

  • Remove uneaten food. You should remove any uneaten fresh foods or soiled dried foods daily. This includes any hay that’s been urinated on or uneaten pellets that managed to get wet.
  • Refill water bowl. Empty and refill the water bowl with fresh water every day. This step will help prevent the buildup of bacteria and encourage better hydration in rabbits.
  • Clean the litter box. Scoop out your rabbit’s poop and the soiled parts of their litter box every day. You don’t need to scrub it down, but this basic cleaning is essential for preventing a build-up of smell from your rabbit’s urine.
  • Quick Sweep up. Do a quick sweep of any hay and fur that are making a mess in and around your rabbit’s enclosure.
rabbit playpen
I always recommend using a pet exercise pen for your rabbit’s enclosure. This gives your rabbit a lot of space and it’s a lot easier to clean.

Enclosure 1: Pet exercise pen 

My preferred setup for a rabbit enclosure is using a pet playpen rather than a traditional rabbit cage. These give your rabbit more space, and the pens are relatively cheap and much easier to clean. You can typically find these in the dog section at pet stores, or you can find these pet playpens online. You’ll want to get a cheap area rug to place underneath the pen and protect the flooring.

If your rabbit is not yet litter trained, you can get large puppy pee pads to wash and reuse. This will make it easy to keep your floor clean while your rabbit learns better potty habits.

  1. Move everything out of the enclosure. This includes all the food bowls, toys, the litter box, and any hiding houses your rabbit uses. You also want to fold up the pen and move it aside to make cleaning easier. As you’re moving everything, check to see if any of the toys are soiled, or all chewed up. You can throw out anything that your rabbit can’t use anymore.
  2. Sweep. After you remove everything, you’ll want to use a dustbin and sweep up any large piles of hay, poop, and fur to prevent any clogs in the vacuum machine.
  3. Vacuum the area. After you’ve done a quick sweep-up, all you have to do is vacuum the area to clean the hay dust and fur.
  4. Wash the rabbit supplies. Now that the enclosure is clean, you want to wash their supplies as well. Clean out any food and water dishes and take the time to clean out the litter box thoroughly. Empty it into the garbage and spray the litter box with a pet-safe all-purpose cleaner.
  5. Place everything back in the enclosure. Now all you have to do is set everything back up the way your rabbit likes it.
rabbit cage with tray on the bottom
Fully enclosed rabbit cages with a tray on the bottom are not ideal for rabbits and are difficult to clean.

Enclosure 2: Fully covered hutch

Fully covered hutches are my least favorite to clean. These are the enclosures where the only way is through a small door. They are set up to make it almost impossible to clean on the inside. These hutches come equipped with a sliding tray at the bottom that the manufacturers expect to catch any rabbit mess. The plan would be for you simply to clean out this tray and be done with it. Unfortunately, that tray is useless.

Why the slide-out tray is useless

You cannot use the tray underneath these rabbit cages because of your rabbit’s feet. For the tray to work, the enclosure needs to have a wired or perforated bottom to allow debris to fall through. 

This type of flooring leads to injured rabbit feet with sore hocks, and it can lead to back problems later on because of the way the rabbit needs to sit. If you have this kind of hutch for your rabbit, you need to cover the wire bottom with towels or mats to protect your rabbit’s feet.

Even if you want to use the tray to catch anything that gets underneath the towel, it typically doesn’t work. Hay pieces are too large to fall through the holes, and urine that misses the litter box will start to rust the wire flooring. Basically, even if this kind of enclosure was not bad for your rabbit’s feet, it’s still ineffective and difficult to clean.

Cleaning a fully covered hutch

  1. Remove everything from inside the hutch. This includes the food and water dishes, toys, and litter box. Throw away any toys that are soiled or all chewed up. You’ll also want to remove the towels and mats you use as bedding. Shake off the bedding into the garbage before putting it in the wash.
  2. Sweep up any remaining hay and poop. Try to sweep up any hay and poop stuck in the wire floor. You may have to remove the tray and turn the cage upside down to remove all the hay, fur, and debris.
  3. Spray the enclosure. Use a pet-safe cleaning spray to disinfect the enclosure floor and walls. If there are any areas with urine stains, try to scrub them to prevent bacteria buildup.
  4. Replace a clean flooring. Once the cage is clean, put clean towels or mats along the bottom as bedding. Avoid the actual product called bedding in pet stores since that is unnecessary and will only make cleaning more difficult.
  5. Clean the supplies. Clean out your rabbit’s food and water dishes before replacing them in the enclosure. You’ll also need to empty the litter tray and scrub it to prevent a bacterial buildup.
  6. Place everything back in the enclosure. Once everything is clean, arrange everything back in the enclosure how your rabbit likes it.
  7. Sweep and vacuum around the cage. Now that the hutch is clean, you’ll probably have a mess in the surrounding area. Sweep up any large hay chunks and vacuum the area to finish cleaning.
rabbit enclosures with easily accessible insides
Enclosures with a fully removable top or wide doors are more easily cleaned because the inside is more accessible.

Enclosure 3: Hutch with removable top

Hutches with a removable top typically have plastic flooring with fencing that you can unclip from the sides. Many dog crates (commonly used as rabbit enclosures) are set up like this. I also include hutches that open entirely from one of the sides with a removable plastic tray lining the bottom in this category. These enclosures are not too difficult to clean since you can comfortably get in and scrub soiled spots.

  1. Remove the wire top of the hutch. Unclip the top of the enclosure and put it aside to give you easy access to the bottom. 
  2. Remove supplies. Take out any food dishes, toys, litter box and any hiding houses your rabbit has. Throw away dirty toys or toys that are chewed up, and remove the mat or towel you have as flooring for your rabbit. Shake off the bedding into the garbage before placing it into the wash.
  3. Sweep up extra hay and poop. Either lift the tray and dump it into the garbage or use a dustpan to sweep up any remaining hay, poop, and fur from the bottom of the enclosure. 
  4. Wipe down the bottom tray. You’ll want to use a cleaning spray to wipe down the hutch’s plastic base. Scrub any urine stains and areas where your rabbit might have missed the litter box.
  5. Clean the supplies. Before placing everything back where it belongs, you’ll want to clean and sanitize the supplies. This includes the food and water dishes and giving the litter box a deep clean.
  6. Place everything back in the enclosure. Replace clean bedding (towels or mats) on the bottom of the enclosure floor and add in all of your rabbit’s supplies.
  7. Sweep and vacuum around the cage. Now that the enclosure is clean, you will likely have a mess in the room. Sweep up the chunks of hay and then vacuum to finish cleaning.

How often should you clean your rabbit enclosure?

If your rabbit is litter trained, you typically only need to deep clean their enclosure once every other week. If your rabbit is particularly clean, you may even be able to go a month without deep cleaning the rabbit pen. As long as you are cleaning the litter box every day and performing those simple daily tasks, your rabbit’s area shouldn’t get dirty too quickly.

However, if your rabbit hasn’t been litter trained, you’ve got a lot of work ahead of you. You will need to clean out their enclosure every day, or at least every other day. Consistent cleaning will be necessary to ensure your rabbit is not living in unclean conditions, preventing urine scald along their legs and underside. Keeping the rabbit enclosure clean will also be essential for encouraging better potty habits when litter training your rabbit.

Finding safe cleaning products for rabbits

Many rabbits like to lick everything that they come across. It’s important to use a cleaning product that does not contain dangerous chemicals so that your rabbit doesn’t lick and ingest anything they shouldn’t.

You can find many pet-safe cleaning products online and in pet stores. These are non-toxic formulas that are safe to use around a home with babies and curious pets. A well-known brand of one of these all-purpose cleaners is Puracy. This product uses a plant-based formula that uses citrus and other plants’ natural cleaning power to keep things clean. (check out the price on Amazon)

You can also make your own pet-safe cleaning solution. Just add equal amounts of water and vinegar (1 cup of water + 1 cup of vinegar)  to create a simple and effective all-purpose cleaner. I don’t like the smell of vinegar, so I also add a few drops of lemon essential oil to make my homemade cleaner smell better. I’ve also found this vinegar solution to eliminate any urine stains on the carpet.

How to make cleaning a rabbit cage easy

If you are consistent with your rabbit’s cleaning routine, it doesn’t take a whole lot of work to keep their area clean. However, there are some ways that you can make the task easier.

  • Get an easy-to-clean enclosure. I recommend getting a pet playpen for your rabbit’s enclosure since this is much easier to clean. It’s typically less expensive and larger than traditional rabbit cages too, so overall I find this to be the best option for house rabbits. (check out the current price)
  • Use towels as bedding. Using the product called bedding is unnecessary for house rabbits. All it does is make cleaning a lot more complicated. Instead, use towels or newspaper along the bottom of the enclosure to give your rabbit’s feet some traction. Towels also make it much easier to clean if your rabbit is not litter trained yet.
  • Let your rabbit explore while you clean. Some rabbits get upset when you try to clean their home. It’s best if you can give them time out to exercise and explore while you get the task done so that you don’t have to worry about an angry rabbit snapping at your hands.

Cleaning hay

Be careful when cleaning the hay out of your rabbit’s enclosure. Hay is very good at clogging any drains and pipes it tries to go through. Never try to clean out hay into a bathtub. You will end up with clogged drains.

Instead, take the time to sweep up the hay with a dustbin first. Then vacuum any leftover small hay pieces and dust. Use a vacuum cleaner that has removable tubes and a clear container. This will help you detect when the vacuum is clogged. Then you can simply remove the tube and unclog it without too much hassle. I use this vacuum cleaner, and it’s still working five years later!

If you use any towels in your rabbit enclosure, make sure to shake off any hay before putting them into the wash. This step will prevent a clog in the washing machine drain. It will also help the dust bin from filling up quite as quickly.

Disposing of rabbit waste

Typically, you will need to dispose of your rabbit’s waste along with the rest of your trash, sending it to a landfill. Some people will try to flush it down the toilet, but I don’t recommend this since it’s likely to clog up the drains.

Simply shovel your rabbit’s poop and soiled litter into a plastic bag and put it in the trash. I have a small, lidded trash can that I use to try using less plastic in my rabbit care routine. I can fill it up with the lid to prevent the smell from spreading. I’ll go through a plastic bag every week instead of every day.

If you have your own garden or compost heap, you can also choose to use your rabbit’s litter box leavings as fertilizer. Rabbit droppings don’t carry diseases like cat or dog poop can. It’s a safe and nutrient-dense fertilizer to use in a garden. You can either sprinkle the poop directly onto the soil or add it to your own compost bin. However, most commercial composting companies will not accept any kind of animal leavings because of the potential for spreading disease from many other animals. This is only an option if you have your own garden at home.


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Amy Pratt

Amy Pratt is a lifelong rabbit owner who has been specializing with rabbits at the Humane Rescue Alliance. She helps to socialize the rabbits and educate volunteers on the care and behavior of these small mammals.

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