When the weather gets warmer the number of flying insects increases, and many horses are allergic to insect bites.  Horses that are allergic to insect bites have a significant reaction that causes them to scratch and rub their skin, and they are very uncomfortable.  Some will scratch and rub enough to lose hair and even develop severe skin infections. All of this is commonly called sweat itch.  The lesions commonly occur on the midline of the horse’s belly but can occur over the back as well as the main and tail areas.  Treatment of the condition requires insect control, sometimes cortisone to decrease the allergic response, and antibiotics if the horse has an infection.  However, cortisone can only be used short term and it can lead to founder, so it is not a good option in the long term. 

Another option for the allergy may be omega 3 fatty acid supplementation.  This therapy is used in dogs with allergies; researchers at the University of Guelph indicated they tested horses using flaxseed, which is a good source of omega 3 fatty acids.  Horses were fed flax meal daily for six weeks and then some were injected with Culicoides extract, which is one of the flies typically involved with the syndrome.  The horses that were fed the flax meal had a significant reduction in skin reaction compared to horses that weren’t.  If your horse has skin allergies to flying insects, feeding omega 3 fatty acids may help.  The only concern I have about the study is that the horses used were not reported to be allergic to flying insects so although the itching decreased, so I don't know if feeding flax seed will make a significant difference in itchy horses but it is worth a try.