What Is E. Cuniculi in Rabbits? What Are the Symptoms?

E. cuniculi is a microscopic parasite that mainly affects a rabbit’s kidneys, brain, and eyes. The parasite belongs to the microsporidian family, which is closely related to fungi. 

While rabbits are most likely to develop illness from E. cuniculi, other animals—including mice, dogs, cats, guinea pigs, and even humans with severely weakened immune systems—can also carry it. 

Studies suggest 50–70% of rabbits may test positive for E. cuniculi, though many never show symptoms, says Colleen Roman, DVM, RVT, exotic animal veterinarian and founder of AnimALL Mobile Veterinary Service in Atlanta, Georgia.  

That’s because most healthy rabbits can keep the parasite in check—E. cuniculi only tends to cause problems when a rabbit’s immune system is weakened, such as during stress, illness, or in older rabbits, says Rae Porter-Blackwell, DVM, ABVP, a board-certified exotic companion mammal specialist at The Center for Bird and Exotic Animal Medicine in Bothell, Washington, and president-elect of the Association of Exotic Mammal Veterinarians (AEMV). 

When symptoms do show up, they can vary. Some are subtle, like changes in bathroom habits, while others, like a head tilt, are more obvious. 

 Some of the most common signs, which can range from mild to severe, include: 

• Head tilt or “wry neck” 
• Loss of balance or coordination 
• Seizures or tremors 
• Eating less or showing less interest in favorite treats 
• Changes in urination 
• Changes in drinking habits 
• Eye problems, like cataracts or lens issues 
• Lethargy 
• Difficulty grooming 

Because early signs aren’t always obvious, it’s important to watch for small changes in behavior, especially if you have multiple rabbits or a new rescue.  

Even minor shifts in eating, mobility, or grooming can be a sign that you should check in with your vet. 

Rabbits can pick up E. cuniculi in a couple of different ways, usually through everyday interactions. Dr. Roman says the main ways E. cuniculi spreads are through: 

• Horizontal transmission: Ingesting or breathing in spores shed in the urine of infected rabbits. This is the most common way pet rabbits become exposed. 
• Vertical transmission: When a mom passes the parasite to her babies during pregnancy. 

Once inside the rabbit’s body, the parasite can travel through the bloodstream to the brain, kidneys, and eyes.  

There’s no cure that completely wipes out E. cuniculi, but veterinarians can help you and your rabbit manage it.  

Dr. Roman says that treatment often includes: 

• Anti-parasitic medicine, usually fenbendazole (often under the brand name Panacur), given by mouth for several weeks. 
• Supportive care, like fluids, special feeding, and helping rabbits eat if neurological symptoms make it difficult. 
• Symptom management, including anti-inflammatory or other medications for head tilt, seizures, or loss of balance. 
• Quality-of-life support, which can include physical therapy, laser therapy, or acupuncture for mobility issues. 

Dr. Porter-Blackwell says that early detection improves the chances of a good outcome—how well a rabbit responds to treatment often depends on how serious their symptoms are.  

Bunnies with mild signs usually bounce back well, but those with serious nerve or kidney problems might have ongoing health issues. 

That’s why it’s important to contact your vet as soon as you notice anything unusual. 

Recovery from E. cuniculi can take weeks to months, and in some cases, clinical signs may never completely go away, says Dr. Roman.  

At home, you can make life easier for a rabbit recovering from E. cuniculi by: 

• Providing a safe, padded space to prevent injuries, especially for rabbits with head tilt or balance issues. Soft fleece pads, like the Paw Inspired Cage Liner, or small animal playpens with cushioned floors work well. 

• Keeping food, water, and litter boxes easy to reach. Low-entry litter boxes, like the Oxbow Small Litter Pan, and shallow dishes make it easier for rabbits with mobility issues to eat and go to the bathroom. Dr. Roman says you should never leave a rabbit with neurological signs or mobility concerns alone with large water bowls, though, as they have an increased risk of drowning. 

• Helping with grooming and cleaning, since rabbits with mobility problems may not be able to keep themselves clean. 
• Reducing stress with a calm, quiet environment. You might have the urge to separate an infected rabbit from a bonded pair, but Dr. Roman says this can be unnecessarily stressful. Plus, it’s likely the other rabbit is already infected but asymptomatic. 
• Providing soft bedding or heated pads for comfort, particularly if your rabbit has difficulty moving or staying warm. The Ware Small Animal Sleeper Bed is a good option. 

These changes can make your rabbit more comfortable and prevent new issues from popping up while they heal.  

Prevention can be tricky, since many rabbits carry the parasite without ever showing symptoms. However, you can reduce the risk by: 

• Checking breeding conditions: If buying a rabbit, ask the breeder about E. cuniculi testing and living conditions. 
• Testing new rabbits: Before introducing a new rabbit to your home, find out its E. cuniculi status. Dr. Porter-Blackwell says a positive test shouldn’t stop you from adopting, though. She has healthy, E. cuniculi-positive rabbits that live perfectly normal lives. You may just want to separate positive and negative rabbits. 
• Practicing good hygiene: Wash your hands after handling rabbits and clean cages with effective disinfectants, like 0.1% bleach for 10 minutes, 70% ethanol for 30 seconds, or peroxide for 30 minutes if you have had a recent positive rabbit, says Dr. Roman. Make sure to rinse thoroughly and dry after recommended contact time.
• Limiting exposure: Avoid contact with unknown rabbits or potentially infected animals. If you do encounter other animals, wash your hands well before handling your rabbits.

What are the symptoms of E. cuniculi in rabbits? 

A: Symptoms vary but can include head tilt, loss of balance, seizures, kidney problems, and eye issues. Some rabbits carry the parasite without ever showing signs. 

Can a rabbit survive E. cuniculi? 

Yes! In fact, many rabbits never get sick. Symptomatic rabbits can improve with early treatment and supportive care, though severe neurological or kidney problems are harder to treat. 

What cleaner kills E. cuniculi? 

Disinfectants like bleach or peroxide can kill E. cuniculi spores. Regular cage cleaning also helps reduce risk. 

How do you treat E. cuniculi infection? 

There’s no treatment that eliminates E. cuniculi, but veterinarians can help manage it with anti-parasitic medication like fenbendazole, supportive care, and symptom-specific treatments for issues like head tilt or seizures.  

Some rabbits also benefit from physical therapy, laser therapy, or acupuncture.