When Pip started tilting her head slightly to one side, I thought she was just being cute. When she started shaking her head more than usual, I told myself it was probably nothing. Three days later she was listing badly to one side and stumbling when she walked. That trip to the vet could have happened a week earlier if I had known what to look for.

Ear infections in rabbits are common, treatable, and — if caught early — straightforward. The problem is that rabbits are very good at hiding the early stages, and by the time symptoms become obvious, the infection has often spread deeper than it needed to. This post is about helping you catch it earlier.

⚠️ Head Tilt or Loss of Balance? Go to the Vet Today

Any head tilt, circling, or stumbling in a rabbit is a medical emergency. It can indicate an inner ear infection or E. cuniculi, both of which progress quickly. Do not wait. Call your vet now.

Three Types of Ear Infections in Rabbits

Rabbits can develop infections in different parts of the ear, and the location matters for both symptoms and treatment.

Outer Ear — Otitis Externa

The most common form. Infection affects the ear canal from the outer opening down to the eardrum. Usually caused by bacteria or ear mites. Often visible to the naked eye as discharge, redness, or crusting. Responds well to treatment when caught early.

Middle Ear — Otitis Media

Infection moves past the eardrum into the middle ear chamber. More serious. Often develops when an outer ear infection goes untreated. May cause more pronounced head tilt and balance issues. Requires a longer course of treatment and imaging to confirm.

Inner Ear — Otitis Interna

The deepest infection, affecting the structures responsible for balance and hearing. Causes significant head tilt, circling, nystagmus (eyes flicking side to side), and loss of coordination. Frequently linked to Encephalitozoon cuniculi (E. cuniculi), a parasitic infection. This is the level where permanent damage becomes a real concern.

The reason ear infections spread so quickly in rabbits is anatomy: the rabbit ear canal is long, narrow, and curved. It does not drain well. Fluid and debris get trapped, creating exactly the environment bacteria love. By the time you see symptoms on the outside, the infection has usually already established itself deeper than the surface suggests.

Ear Mites vs. Bacterial Infections

These are the two most common causes of outer ear problems, and they look similar at first — which is why a vet diagnosis matters.

Ear Mites (Psoroptes cuniculi)

Mites live on the surface of the ear canal and feed on skin cells and fluids. The hallmark sign is thick, dry, crusty material that builds up in layered sheets — often described as looking like stacked commas or ridges. It is itchy, so you will see a lot of head shaking and pawing at the ears. Mites are treatable and not life-threatening on their own, but the scratches they cause can become secondary bacterial infections if left alone.

Bacterial Infections

Usually caused by Staphylococcus or Pasteurella bacteria. Discharge tends to be wetter, may have a smell, and often looks yellow, white, or gray. Bacterial infections can start after trauma to the ear canal, from moisture trapped after bathing, or as a secondary infection following mites or another illness. They require specific antibiotic treatment — what works for mites will not work here.

The tricky part: you cannot reliably tell which one you are dealing with just by looking. Your vet can take a sample from the ear canal and look at it under a microscope. Five minutes of diagnostic time leads to the right treatment from day one.

Warning Signs to Watch For

Ear infections rarely appear suddenly. They start subtle and escalate. Here is what to look for, in roughly the order it typically shows up:

  • Head shaking — more than the occasional shake, especially if it is repeated
  • Pawing at ears — scratching or rubbing ears against the floor, furniture, or their own paws
  • Crusty discharge — white, yellow, or gray buildup inside the ear flap or deep in the canal
  • Odor — a smell coming from the ear that is stronger than normal rabbit ear smell
  • Ear sensitivity — flinching or pulling away when you touch or approach the ear
  • Head tilting — holding the head at an angle, usually to one side
  • Circling — walking in circles, especially in one direction
  • Loss of balance — stumbling, wobbling, falling over, inability to hop straight
  • Eye flickering — eyes jerking side to side (nystagmus), a sign of inner ear involvement
  • Loss of appetite — secondary effect of feeling unwell and dizzy

The first four are early stage. Head tilting through the end of the list are mid-to-late stage. Once you see head tilt, you are past the easy window.

What the Vet Will Do

Your vet appointment for a suspected ear infection will typically go like this:

  1. Physical exam — including looking at the ears with an otoscope to see how deep the inflammation goes and whether the eardrum is visible or obscured
  2. Ear cytology — taking a sample from the ear canal and looking at it under a microscope to identify mites, bacteria, or yeast
  3. Culture — in persistent or severe cases, the vet may culture the discharge to identify the exact bacteria and which antibiotics will work
  4. Neurological assessment — checking for head tilt, circling, and nystagmus to determine whether the inner ear is involved
  5. Imaging — for significant head tilt or balance issues, X-rays or a CT scan may be recommended to see the middle and inner ear structures and check for fluid, bone involvement, or E. cuniculi lesions in the brain or kidneys

If E. cuniculi is suspected, your vet may also order a blood test or PCR test. The parasite itself is common in rabbits — many carry it with no symptoms — but when it activates in the nervous system or eyes, it requires specific treatment with anti-parasitic drugs alongside the ear treatment.

Treatment: What to Expect

Treatment depends on how deep the infection is, but here is the general outline:

Outer Ear Infections

Topical antibiotic or antifungal ear drops, sometimes combined with a steroid to reduce inflammation. Course is typically 7–14 days. Your vet may clean the ear with a safe solution first — do not attempt to clean the ear canal yourself with anything not prescribed.

Middle or Inner Ear Infections

Topical drops plus oral antibiotics, often for 3–6 weeks. Anti-inflammatory medication may be prescribed to reduce swelling in and around the ear canal. Pain management may also be part of the plan — do not skip this, even if your rabbit seems fine. If E. cuniculi is involved, an anti-parasitic like fenbendazole (Panacur) will be added to the protocol.

One thing that surprised me the first time: the ear drops often seem to bother Pip more than the infection did. She would shake her head and fuss after application. That is normal. Do not stop treatment early because your rabbit seems upset by the drops — the infection will come back, and it will be harder to treat a second time.

Never use over-the-counter ear drops meant for dogs or cats. Rabbit ears have a specific pH and microbiome, and the wrong product can make things worse.

The E. Cuniculi Connection

E. cuniculi comes up a lot in discussions about rabbit ear infections, and with good reason. The parasite can cause inflammatory lesions in the brain, eyes, kidneys, and — importantly for this topic — the inner ear. When it affects the vestibular system, it produces symptoms that look exactly like a bacterial inner ear infection: head tilt, circling, loss of balance.

This is why a proper diagnosis matters. A bacterial ear infection and an active E. cuniculi infection are treated very differently. Treating one as the other wastes time, lets the real problem advance, and may cause unnecessary suffering for your rabbit.

E. cuniculi is transmitted through urine, often from mother to kit during pregnancy or from environmental exposure to infected urine. Many rabbits carry the spores their whole lives with no symptoms. Stress, illness, or immune system changes can trigger active infection. There is no way to fully prevent exposure, but keeping rabbits in clean conditions and minimizing stress reduces the risk of activation.

Prevention: What You Can Do

You cannot eliminate all risk — rabbits are prone to ear issues, and some is just bad luck. But there are things that genuinely help:

  • Regular ear checks — take a look inside the ear flaps every couple of weeks. Learn what normal looks like so you notice changes early
  • Keep ears dry — moisture in the ear canal creates the exact environment bacteria and fungi need. After baths or if your rabbit gets wet, make sure the ear area is thoroughly dried
  • Parasite prevention — talk to your vet about mite prevention, especially if your rabbit has had mites before or lives with other rabbits who go outdoors
  • Address symptoms early — that first head shake is your cue. Waiting is the thing that turns a simple outer ear issue into a middle ear problem
  • Spay or neuter — unspayed does have higher rates of certain reproductive cancers that can affect surrounding tissues, and neutering reduces stress-related immune suppression

Recovery: What to Expect at Home

Once your vet has diagnosed and prescribed, recovery mostly happens at home. Here is what that looks like:

  • Administer medication on schedule — set a daily alarm if needed. Ear drops and oral antibiotics both work best with consistent dosing
  • Keep your rabbit comfortable — if there is significant head tilt or balance loss, keep your rabbit in a small, safe space where falling into furniture or down stairs is not a risk. Line the floor with towels or fleece for grip
  • Support eating and drinking — a dizzy rabbit may have trouble navigating to their water bowl. Place food and water close by, at head-height if possible, and offer hay and leafy greens they can reach without moving far
  • Monitor for improvement — most outer and middle ear infections start improving within 3–5 days of treatment. If you do not see any change by day 5, call your vet
  • Finish the full course — even if your rabbit looks completely better, finish all prescribed medication. Stopping early is the most common reason ear infections come back
  • Watch for residual head tilt — mild head tilt can persist for weeks after the infection clears, as the balance structures heal. This is not necessarily a sign of ongoing infection — your vet can help you assess

Most rabbits recover fully from outer and middle ear infections with prompt, appropriate treatment. Inner ear infections take longer and may leave some residual head tilt, especially if treatment was delayed. But even rabbits with permanent mild head tilt can live full, comfortable lives — they just adapt.

The Bottom Line

Ear infections in rabbits are common, treatable, and — in most cases — fully recoverable if you catch them early. The key is knowing what to watch for, not waiting to see if it gets better on its own, and getting to a rabbit-savvy vet quickly when symptoms appear.

If your rabbit is tilting their head, shaking their head repeatedly, or showing any loss of balance — make that call today. It is never an overreaction, and it is almost always the right call.