Danielle,
Sorry for the delay in getting back to you. It is increasingly difficult for me to keep up with the questions that come in. I hope by now your horse has not chewed himself up. Dr. Katherine Houpt from Cornel University has done a lot of research on this subject, so she would be a good resource for you to check out.
Horses that self-mutilate (bite at their own flesh causing open wounds) are generally either in severe pain or severe stress. It may be that your stallion began this behavior when he was isolated and frustrated and now it is habitual behavior. The obvious solution is to resolve the pain or stress and that usually makes the behavior go away. If not, you can put a neck cradle on the horse to prevent him from reaching to his sides or legs with his mouth. It is a bunch of dowels strapped together that you buckle around his neck when he is in the stall. They can be bought from just about any vet catalogue and would probably be found in the bandaging section. I don't think it is a good idea to have a neck cradle on him when he is with other horses.
To quote from Dr. Houpt's book on animal behavior: "Self-mutilation is a very common behavior problem. Although it occurs in both sexes, it is much more common in stallions. The behavior consists of biting at or actually biting the flanks or, more rarely, the chest. The horse usually squeals and kicks out at the same time. The signs mimic those of acute colic, but can be differentiated because self-mutilation does not progress to rolling or depression and is chronic. The cause of the behavior is unknown, but because it usually responds to a change in the social environment it is probably caused by sociosexual deprivation. Most breeding stallions do lead similarly deprived lives in that they are kept in stalls in isolation from other horses, particularly from mares, but do not self-mutilate. .... Castration usually, but not always tops self-mutilation." There are a few more paragraphs about it in her book and I would be happy to fax you a copy of that or you can get the book: Domestic Animal Behavior for Veterinarians and Animal Scientists, by Katherine Albro Houpt, VMD. PhD, Iowa State University Press. I got my copy from Knight Equestrian Books, (207) 882-5494.
I have seen a handful of horses in my career that are self-mutilators. The most distinguishable case was a mare being trained to jump by a brutal trainer who rode her in sides reins with her nose to her chest while jumping. She began to bite her chest while being ridden until both sides of her shoulder were dripping with blood at the end of every course of jumps. Eventually the owner figured out that is was from the pain and stress the trainer inflicted and removed the horse and the problem went away. I would have like to put the trainer into similar kinds of pain and stress and see how he responded. Oddly enough, this person is still training horses, or so I've heard. The other horses were stallions with exacerbating medical conditions that had them in pain. When the horses were brought back to a healthy condition, the self-mutilation went away.
The best you can do is try to find a social arrangement that relieves your horse's anxiety and/or use the neck cradle if you cannot prevent it. Also, make sure he does not have other conditions that may be causing him pain like chiropractic issues or disease. It may be that the behavior diminishes with time. This is a difficult problem and I wish you all the luck in resolving it.
JG
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Animals in Translation Book: http://shop.juliegoodnight.com/shop/baanimalsintranslation.html
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