Editor’s Note: This is from Understanding Equine Preventive Medicine by author and veterinarian Bradford G. Bentz, VMD. 

Vaccination may be associated with a limited number of adverse effects. Muscle swelling, stiffness, mild fever, anorexia, and lethargy are all potential side effects.  Systemic signs of malaise may be seen more commonly with the administration of intramuscular preparations of inactivated influenza virus vaccine than with others. This is thought to be due to reaction at the injection site. It is therefore recommended that horses do not receive any vaccination within two weeks of performance, sales, or shipment. It is further recommended that horses do not receive inactivated (killed) equine influenza vaccines within three weeks of international shipment.

Other adverse reactions that have been associated with the administration of a vaccine include anaphylaxis and local irritation to the tissue, but these are uncommon. Anaphylaxis is a life-threatening emergency requiring immediate veterinary attention and possibly the administration of epinephrine, a cardiac drug that improves blood pressure  while increasing heart rate and contractility.

Local tissue reactions are generally self-limiting but may benefit from oral non-steroidal anti-inflammatory drugs such as phenylbutazone or flunixin meglumine, warm compresses, topical DMSO gel, and gentle exercise. Local reactions might be minimized by vaccines deep in the semimembranosus and semitendinosus muscles of the hind leg and by allowing the horse to exercise after vaccination