Encephalitozoon cuniculi

Encephalitozoon cuniculi (E cuniculi) is a commonly referenced disease in rabbits, and is reported to be quite widespread in pet rabbit populations. However, clinical disease is hard to differentiate from previous infection, and their may be other causes at work.

E cuniculi is a single celled microsporidian pathogen, passed through ingesting or inhaling infected urine or in utero transmission. E cuniculi commonly affects the brain, spine, eyes, and kidneys, forming cysts or granulomas, preventing complete resolution of infection.

The main signs of E cuniculi that rabbits are presented for include :

  • Neurological disease
    • Head tilt / Loss of balance
    • Rolling
  • Renal disease
    • Polyuria/polydipsia
  • Ophthalmic disease
    • Cataracts
    • Phacoclastic uveitis – white/pink/fluffy mass


It was mentioned earlier that Encephalitozoon cuniculi can be quite difficult, this is because the best method of detecting whether E cuniculi is affecting the brain, spine, eyes or kidneys is PCR on post mortem tissues.

This is not an option in live patients.

In some places, a PCR of urine, faeces or tissue may be available. But unfortunately, it’s not an option in Australia.

Other tests can only diagnose previous infection, not whether E cuniculi is currently CAUSING the symptoms observed.

You can perform serology using either an Immunofluorescent Antibody Assay (IFA) or an Enzyme Linked Immunosorbent Assay (ELISA) tests. If your rabbit patient is seropositive, then your rabbit has been exposed and you should treat appropriately. If seronegative, there is another source for the clinical disease, which needs to be determined.


There is no way to cure Encephalitozoon cuniculi, however you can limit the impact of the infection with:

  1. Fenbendazole – anti-parasitic – it’s difficult to completely eliminate E cuniculi, however you can severely decrease the amount present in your bunny patient with long courses of cuniculi. This may need repeating every 6 months for a shorter course to prevent recurrence of clinical signs.
  2. Supportive care – fluids, analgesia (if required), warmth, soft safe environment to prevent trauma from rolling or loss of balance.

Encephalitozoon cuniculi is a tricky disease to manage, as it cannot be cured and is difficult to definitively diagnosed. However, if caught early, can be managed long term.

  • Melbourne Rabbit Clinic. What is EC? MRC.
  • Melbourne Rabbit Clinic. Rabbit Clinic Manual. MRC. 2018.

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