Although the disease is called Equine Encephalosis, it is not primarily a neurological disorder.

Most infections produce only mild clinical signs.

Common signs include:

• Fluctuating fever (typically lasting 2–5 days)
• Inappetence
• Increased heart rate
• Increased respiratory rate
• Nasal congestion
• Red-brown discoloration of the mucous membranes

Less common but more severe signs include:

• Swelling of the lips and eyelids
• Respiratory distress
• Petechial haemorrhages of the conjunctiva
• Abortion during the first five months of gestation

Neurological signs are uncommon but may include:

• Hindquarter ataxia
• Convulsions
• Hyperexcitability
• Depression

The mortality rate is generally low, affecting approximately 5% of infected animals.