1. Home
  2. Small Pet
  3. Rabbit

Treatment And Prevention Of E. Cuniculi In Rabbits

Kevin Wright, DVM, DABVP
By Kevin Wright, DVM, DABVP
Updated
Apr. 30, 2025
A veterinarian holding a rabbit

Photo by leaf/iStock/Getty Images Plus

If you’ve not yet heard of it, encephalitozoon cuniculi, called E. cuniculi (EC), is a tiny parasite that lives inside infected rabbits, is a notable cause of diseases and can be passed to humans, especially those already susceptible to illness. It is a microsporidian, a type of organism more closely related to fungi than to protozoans or animals.

Unfortunately, almost all pet rabbits have been exposed to the organism at some point. The infection is passed on through spores shed in an infected mammal’s urine, and even if you practice good hygiene, there’s a chance your rabbit still might contract EC. They can acquire the disease from ingesting the spores, inhaling the spores or having the spores settle on their eyes. Also, infected does can pass EC on to their unborn babies.

If you rabbit is ill, E. cuniculi is a disease that you and your veterinarian must consider, and EC screening should be part of any pet rabbit’s wellness program. If your rabbit develops signs of EC, early treatment is more likely to help than care started even several days after the first signs of illness.

Treating E. Cuniculi in Rabbits


Unfortunately, no specific medications target microsporidians. Developing such a medication was not a priority for pharmaceutical companies until human patients with AIDS started to develop infections by unusual organisms, and then some cases of microsporidiosis were found in seemingly healthy humans.

Albendazole, fenbendazole and oxfendazole medications are used to treat nematodes and other parasitic worms, and they happen to offer some efficacy against EC. Though it is the drug of choice in people, Albendazole has a negative reputation in the pet rabbit community.

While Albendazole does have adverse side effects, no peer-reviewed studies have proven that the alternatives, fenbendazole and oxfendazole, do not have similar side effects in EC-infected rabbits. The only peer-reviewed treatment study on E. cuniculi in rabbits used fenbendazole, and, despite the flaws in this study, it has been the standard for deriving treatments for EC-positive rabbits. This, combined with the drug’s availability, affordability, shelf-life and acceptability to most clients over albendazole, is why I routinely prescribe fenbendazole for EC rabbits.

Due to the nature of the EC lesions, some vets give corticosteroids to EC rabbits to reduce the brain inflammation. The risk with this treatment is that corticosteroids might suppress the immune system to the point that EC or other infectious organisms may create additional problems.

For that reason, some veterinarians choose to go with nonsteroidal anti-inflammatory drugs (NSAIDS), such as meloxicam. Corticosteroids such as prednisone or dexamethasone seem to be more effective than meloxicam, but it might be that the meloxicam dose advised for rabbits does not provide adequate blood levels.

No study has definitively answered how much meloxicam a rabbit should receive to control inflammation or what dose of corticosteroid is best. Never give a rabbit a corticosteroid with meloxicam, as this can cause stomach ulcers!

Some vets give EC rabbits doxycycline, an antibiotic with some anti-inflammatory properties, along with corticosteroids or meloxicam. Red palm oil and other balanced omega fatty acid mixtures may help reducing inflammation. I’ve used Booster, a proprietary product from Harrison’s Pet Products that contains red palm oil and a substance with antibiotic properties, with EC-infected rabbits, but it is difficult to evaluate its overall impact given the other medications given in the course of treatment.

Ponazuril, a medication effective against coccidia, and ivermectin, a medication effective against nematodes and other invertebrate parasites, are given by some veterinarians. As well, Lufenuron, a flea treatment formulated to inhibit chitin production, has been tried on the assumption that one part of the microsporidian life cycle, the endospore, has chitin.

A combination treatment of pyrimethamine, sulfadiazine, folic acid and meloxicam has been tried on E. cuniculi in rabbits extrapolating from work done on horses with certain parasites. Enrofloxacin and chloramphenicol, both antibiotics, sometimes are given as well.

Many other medications have been tried, but it is unclear if any of these treatments include anti-microsporidian properties because no peer-reviewed, controlled studies or peer-reviewed, retrospective studies have been done to assess the validity of the claims that are made. Furthermore, all of these medications are extra-label use in rabbits.

Nursing Care of EC Rabbits

Nursing care for rabbits with EC includes assistance feeding your pet with a liquid diet, providing subcutaneous fluids if she cannot stay well-hydrated and applying eye lubrications. If your rabbit is unable to clean her rump area from night feces and other debris, doing it for her helps prevent scalding.

Meclizine or other anti-nausea/anti-vertigo medications may help improve a rolling rabbit’s attitude and appetite. A soft, cushioned environment, like a large plastic tub lined with towels or soft cushions, is needed for rolling rabbits. And a rabbit with a head tilt will benefit from massage to help relieve the stress of the abnormal muscle posture.

It can take weeks for a rabbit to show significant improvement. Many end up with a permanent head tilt but otherwise seem to enjoy a normal quality of life.

Rabbits with cataracts can undergo surgery to remove the problem lens. This surgery is costly, and not every veterinary ophthalmologist is willing to work on rabbits. However, if the infected lens is left in place it might rupture and cause further inflammation in the eye, even with prophylactic drug therapy that includes fenbendazole.

Preventing E. Cuniculi Infection


There is no vaccine to prevent E. cuniculi in rabbits, and EC spores stay alive for months under the right conditions. Fortunately, chlorine bleach and other readily available disinfectants kill the spores.

To combat EC spores, follow these steps.

  1. Thoroughly clean your rabbit’s environment to remove obvious urine, feces and other organic dirt, such as pellets and hay.
  2. Wash her cage, food bowls and other furnishings in hot, soapy water to remove the invisible dirt. Rinse all these items in hot water.
  3. Disinfect the clean items by applying a diluted solution of bleach (1:32) to each one. Let them sit for 15-30 minutes before rinsing them again in fresh hot water.
  4. Wash all towels or cloth items in hot, soapy water and bleach. To avoid fading your cloth items, use a commercial disinfectant such as Roccal. Vinegar often is touted as a safe disinfectant, but it may not kill EC spores.

EC spores can be anywhere your rabbit was, such as the couch, carpet or bed, and the spores can float around in the air and reach other places, too. If you have an EC-positive rabbit, consider your whole household contaminated.

This means is that any rabbit coming into your household is being exposed to the EC spores, and any visitors who live with rabbits might pick up spores and bring them back to their own pets. You needn’t be considered a pariah, though, because almost every pet rabbit has been exposed to EC at some point in her life and either successfully fought the infection so she is not ill or already contracted the infection and has shown signs of illness.

Controversy exists about how to manage EC-positive rabbits. I recommend that any EC-positive rabbit, whether or not she shows signs of illness, is treated monthly with a 3- to 5-day course of fenbendazole. Other rabbits in the household can get monthly doses.

Put any new rabbits entering your household on the same monthly dose. Also, any time a rabbit undergoes stress, such as travel, boarding or other unusual activity, I put her on prophylactic fenbendazole.

A coordinated effort to provide major funding for EC research of pet rabbits is needed if we are to make any advances in its prevention and treatment.

Attributions


Kevin Wright, DVM, DABVP

Kevin Wright, DVM, DABVP

Related articles
  • Hare vs. Rabbit: How Are They Different and How Are They Similar?
    Hare vs. Rabbit: How Are They Different and How Are They Similar?

  • Rabbit Poop Guide: What Your Bunny’s Poop Means
    Rabbit Poop Guide: What Your Bunny’s Poop Means

  • Can Rabbits Eat Cabbage?
    Can Rabbits Eat Cabbage?

  • Can Rabbits Eat Blackberries?
    Can Rabbits Eat Blackberries?
Skip to searchSkip to main content
Not in the U.S?

Not shopping in the U.S. or plan on shipping to a Canadian address?

Continue to Canada site
Use App
24/7 HelpHelp
Get help from our experts 24/7
1-800-672-4399
    • Track Order
    • -
    • FAQs
    • -
    • Contact Info
    AccountAccount
    Sign InNew Customer? Start here
    • Account
    • Orders
    • Manage Autoship
    • Favorites
    • Buy Again
    • Prescriptions
    • Pet Portal
    • Connect with a Vet
    • Pet Insurance Dashboard
    • My Rescues
    • Create a Pet Profile
    CartCart
    Your cart is empty.
    Something missing? Sign in to see items you may have added from another computer or device.
    Not in the U.S?

    Not shopping in the U.S. or plan on shipping to a Canadian address?

    Continue to Canada site
    Use App
    24/7 Help
    Get help from our experts 24/7
    1-800-672-4399
      • Track Order
      • -
      • FAQs
      • -
      • Contact Info
      AccountAccount
      Sign InNew Customer? Start here
      • Account
      • Orders
      • Manage Autoship
      • Favorites
      • Buy Again
      • Prescriptions
      • Pet Portal
      • Connect with a Vet
      • Pet Insurance Dashboard
      • My Rescues
      • Create a Pet Profile
      CartCart
      Your cart is empty.
      Something missing? Sign in to see items you may have added from another computer or device.
      Food
      • Dry Food
      • Wet Food
      • Fresh Food & Toppers
      • Veterinary Diets
      • Shop by Health Condition
      • Puppy Food
      Treats
      • Bones, Bully Sticks & Naturals
      • Soft & Chewy Treats
      • Dental Treats
      • Biscuits & Cookies
      • Long-Lasting Chews
      • Jerky Treats
      • Freeze-Dried & Dehydrated
      Toys
      • Plush Toys
      • Chew Toys
      • Fetch Toys
      • Treat Dispensing Toys
      • Puzzle Toys
      • Rope & Tug Toys
      Supplies
      • Crates, Pens & Gates
      • Beds
      • Leashes, Collars & Harnesses
      • Bowls & Feeders
      • Clothing & Accessories
      • Carriers & Travel
      • Training & Behavior
      Dog DealsNew Dog SuppliesPet Parent SuppliesShop all Dog
      Grooming
      • Brushes & Combs
      • Shampoos & Conditioners
      • Grooming Tools
      • Paw & Nail Care
      • Ear Care
      • Skin Care
      Cleaning & Potty
      • Pee Pads & Diapers
      • Poop Bags & Scoopers
      • Cleaners & Stain Removers
      • Vacuums & Steam Cleaners
      Health & Pharmacy
      • Flea & Tick
      • Anxiety & Calming Care
      • Allergy & Itch Relief
      • Vitamins & Supplements
      • Heartworm & Dewormers
      • Pharmacy & Prescriptions
      • DNA Testing Kits
      Gift Cards
      Popular Brands
      Purina Pro Plan
      Hill's
      Blue Buffalo
      Frisco
      Royal Canin
      Bark
      Elevate your puppy's diet. Get adventure-ready with ORIJEN puppy. Shop now.
      Food
      • Wet Food
      • Dry Food
      • Everyday Favorites
      • Shop by Health Consideration
      • Veterinary Diets
      • Highest Quality Food
      • Food Toppers
      Litter
      • Clumping
      • Scented
      • Unscented
      • Natural
      • Lightweight
      Treats
      • Crunchy Treats
      • Lickable Treats
      • Soft & Chewy Treats
      • Dental Treats
      • Catnip & Cat Grass
      Toys
      • Interactive & Electronic Toys
      • Teasers & Wands
      • Balls & Chasers
      • Catnip Toys
      • Plush & Mice Toys
      Cat DealsPet Parent SuppliesShop all Cat
      Supplies
      • Litter Boxes & Accessories
      • Cat Tech & Smart Home
      • Beds
      • Carriers & Travel
      • Bowls & Feeders
      • Collars, Leashes & Harnesses
      • Grooming
      Trees & Scratchers
      • Trees & Condos
      • Scratchers & Scratching Posts
      • Wall Shelves
      • Window Perches
      Health & Pharmacy
      • Flea & Tick
      • Anxiety & Calming Care
      • Allergy & Itch Relief
      • Vitamins & Supplements
      • Urinary Tract & Kidneys
      • Pharmacy & Prescriptions
      • Test Kits
      Gift Cards
      Popular Brands
      Tiny Tiger
      Shop Blue Buffalo
      Shop litter robot
      Shop Temptations
      Shop Hill's Science Diet
      Shop Purina Pro Plan
      Help support their urinary health with Royal Canin Urinary nutrition. Shop now.
      Horse
      • Feed
      • Treats
      • Health & Wellness
      • Vitamins & Supplements
      • Fly Control
      • Prescription Medications
      • Vaccines
      Chicken
      • Feed
      • Treats
      • Nesting & Egg Supplies
      • Coops & Runs
      • Feeders, Waterers & Deicers
      Farm Animal
      • Cattle
      • Goat
      • Pig
      • Sheep
      • Llama & Alpaca
      Wild Bird & Wildlife
      • Wild Bird
      • Squirrel & Critter
      • Duck & Waterfowl
      • Deer
      Small Pet
      • Rabbit
      • Guinea Pig
      • Hamster
      • Ferret
      Pet Bird
      • Food
      • Treats
      • Toys & Perches
      • Litter & Nesting
      • Cages & Accessories
      Fish
      • Tanks & Aquariums
      • Food
      • Filters & Media
      • Decor & Substrate
      • Water Care
      Reptile & Amphibian
      • Live Feed
      • Food & Treats
      • Tanks & Terrariums
      • Heating & Lighting
      • Substrate & Bedding
      Gift Cards
      Popular Brands
      Shop Buckeye
      Shop Animed
      Shop Cosequin
      Chewy Chick Days deals. Save on feed & supplies for every life stage. Shop now.
      Prescriptions
      Order your pet's prescription items.
      How it works
      Shop all Pharmacy
      Health Services
      Chewy Vet Care
      Chat free with our vet team
      CarePlus Insurance & Wellness Plans
      Compounded Medications
      Choose from a variety of flavors, strengths, and forms for your pet or horse.
      Learn about compounding
      Dog
      • Flea & Tick
      • Heartworm
      • Pain Relief & Arthritis
      • Antibiotics
      • Allergy Relief
      • Anxiety & Calming
      • Ear & Eye Care
      • Diabetes Care & Insulin
      Cat
      • Flea & Tick
      • Dewormers & Parasiticides
      • Ear & Eye Care
      • Antibiotics
      • Allergy Relief
      • Urinary Tract & Kidneys
      • Pain Relief & Arthritis
      • Diabetes Care & Insulin
      Horse
      • Anti-inflammatory & Musculoskeletal
      • Vitamins & Electrolytes
      • Skin & Coat Care
      • Antibiotics
      • Metabolic & Endocrine
      • Allergy & Immune
      • Behavioral Support & Sedatives
      • Reproductive Care
      Expert Health Tips
      • PetMD
      Connect with a Vet
      Free chat or live-video advice from our licensed veterinary team.
      Learn more
      CarePlus Insurance & Wellness Plans
      Give your pet the best possible health coverage with wellness and insurance plans.
      Learn more
      Chewy Vet Care
      Exceptional in-person routine and urgent care from our compassionate veterinary teams.
      Schedule a visit
      Learn
      How We Give Back
      We've donated more than $100M in products to rescue animal centers.
      Learn more
      Donate to a Rescue
      You can help us make an impact by donating items to your local shelter.
      Find a Rescue
      Find Pets to Adopt
      Search thousands of pets from shelters and rescues in Chewy's network.
      Find Pets
      Join Our Network
      Join our network to access benefits and resources that’ll help more pets.
      Join Now
      Today's Deals
      • Our experts are available 24/7:We're here 24/7:
      • 1-800-672-4399
      • United States
      • About
      • Investor Relations
      • Affiliates
      • Jobs
      • FAQs
      • Learn
      • Give Back
      • Gift Cards
      • Sell on Chewy
      Download iOS appDownload Android app
      Go to ACHC pharmacy accreditationLegitscript ApprovedCompounding Pharmacy Approved
      • Copyright © 2025, Chewy, Inc.
      • Terms of Use
      • Privacy Policy (Updated Oct 8, 2024)
      • Interest-Based Ads
      • Accessibility
      • California Supply Chains Act
      • Vendor Compliance
      Download phone image
      Get the Chewy app
      Download iOS appDownload Android app
      We're here 24/7
      1-800-672-4399
      United States
      Copyright © 2025 Chewy, Inc.
      Terms-Privacy (Updated Oct 8, 2024)-Accessibility
      California Supply Chains Act-Vendor Compliance
      About-Investor Relations-Jobs-Learn
      Give Back-Gift Cards-Sell on Chewy