Encephalitozoonosis in Rabbits
What is encephalitozoonosis?
Encephalitozoonsis is an infection that can affect rabbits’ kidneys, eyes, stomach, and nervous systems. It is caused by an organism called Encephalitozoon cuniculi or E. cuniculi, a microscopic parasite. It is an intracellular parasite, meaning it must live within a cell of the host animal. Encephalitozoonosis can affect rabbits, mice, hamsters, dogs, cats, guinea pigs, and humans. It usually causes a latent condition in rabbits, meaning most infected rabbits show no symptoms.
How could my rabbit become infected with encephalitozoonosis?
Rabbits are infected in one of two ways:
1. From the urine of other infected rabbits. Your rabbit may eat a contaminated food source that contains spores of this organism that were passed in an infected rabbit’s urine. Or your rabbit may lick its feet after hopping in an area where an infected rabbit lived. The spores reproduce in your rabbit (the new host) until your rabbit passes them in their urine, continuing the cycle.
2. From their mother. A mother rabbit can pass E. cuniculi to her unborn baby (in utero infection). Rabbits infected in utero may produce infections within the lens of the eyes. These lesions or infections look like white clumps inside the eye.
What are the clinical signs of encephalitozoonosis in rabbits?
Most infected rabbits do not show any signs of encephalitozoonosis until they are older, become stressed, or are immunocompromised. Some rabbits never show any signs. If your rabbit is infected and signs do develop, you may see any of the following:
- Heavy white plaques/growths inside one or both eyes (hypopyon)
- A head tilt, due to involvement with the central nervous system
- Nystagmus (eye twitching)
- Anorexia (lack of appetite)
- Gastrointestinal stasis (slowed or stopped gut movement)
- Difficulty walking
- Rolling, unable to stand on all four legs
- Tremors and seizures
How is encephalitozoonosis in rabbits diagnosed?
Your veterinarian can make a presumptive diagnosis based on clinical signs and by ruling out other possible diagnoses. Sometimes, a diagnosis is presumed based on a rabbit’s response to treatment. There are also blood tests that can detect antibodies to the E. cuniculi organism. A positive test with clinical symptoms confirms the diagnosis of an E. cuniculi infection. Cases in which rabbits show no symptoms are extremely difficult to diagnose with blood tests.
After a rabbit passes away, a necropsy can be performed, and sections of the kidneys and/or other organs can be submitted to a pathologist to search for the E. cuniculi organism. If there is more than one rabbit in the household, the other rabbits should be tested and/or treated.
How is encephalitozoonosis treated?
There are several effective drugs to treat encephalitozoonsis; however, there are no specific anti-E. cuniculi drugs. Two anti-protozoal medications, fenbendazole (Panacur®) and ponazuril (Marquis®), have shown effectiveness in treating most mild to moderate cases of E. cuniculi. Severely infected rabbits often have little to no response to medical treatment.
Cases involving ocular infection must referred to a veterinary ophthalmologist if surgery is recommended. The growth in the eye will not go away with medical treatment alone. With medical treatment, these ocular lesions will stabilize and may not require more aggressive treatment.
If your rabbit declines in health, humane euthanasia may be a loving consideration.
Can encephalitozoonosis infect humans?
Encephalitozoonosis infection in humans is poorly understood. The condition has been described in a few cases in people, and it is reported that very young, elderly, and immunocompromised people are most at risk. To reduce risk, it is important to always wash your hands after handling any animal and before eating or preparing food.
© Copyright 2025 LifeLearn Inc. Used and/or modified with permission under license. This content written by LifeLearn Animal Health (LifeLearn Inc.) is licensed to this practice for the personal use of our clients. Any copying, printing or further distribution is prohibited without the express written consent of LifeLearn. This content does not contain all available information for any referenced medications and has not been reviewed by the FDA Center for Veterinary Medicine, or Health Canada Veterinary Drugs Directorate. This content may help answer commonly asked questions, but is not a substitute for medical advice, or a proper consultation and/or clinical examination of your pet by a veterinarian. Please contact your veterinarian if you have any questions or concerns about your pet’s health. Last updated on Jun 27, 2025.