A rabbit holding its head to the side, a condition often referred to as "head tilt" or "wry neck," can be caused by several underlying issues. Some of the common causes include:

1. **Ear Infections**: Bacterial or fungal infections in the inner or middle ear can lead to inflammation and affect the rabbit's balance, causing it to hold its head to the side.

2. **E. cuniculi**: This is a parasitic infection caused by the protozoan *Encephalitozoon cuniculi*. It can affect the brain and kidneys and lead to neurological symptoms, including head tilt.

3. **Head Trauma**: Injury to the head or neck can result in damage to the structures responsible for balance and orientation, leading to head tilt.

4. **Toxins**: Exposure to certain toxins can affect the nervous system, causing neurological symptoms such as head tilt.

5. **Tumors**: Growths in the brain or ear structures can put pressure on nerves and lead to head tilt.

6. **Stroke**: A cerebrovascular accident, although less common in rabbits, can cause sudden onset of neurological symptoms, including head tilt.

7. **Vestibular Disease**: Disorders affecting the vestibular system (part of the inner ear and brain responsible for balance) can cause a rabbit to tilt its head.

If you notice a rabbit with head tilt, it is important to seek veterinary care promptly. A veterinarian can diagnose the underlying cause and recommend appropriate treatment, which may include antibiotics for infections, anti-inflammatory medications, antiparasitic treatments, or supportive care depending on the diagnosis. Early intervention can improve the chances of recovery and reduce the risk of permanent damage.