They have been shown to be safe for the horse as well as effective. It is a matter of what works on your horse. Sprays are easiest to apply but care must be taken to avoid getting the product into the eyes. Wipe-on products can also be used over the whole horse. Many people prefer to use all-natural products with active ingredients such as citronella and pyrethrins.
Many people report that feeding their horse apple vinegar makes the horse less attractive to flies.
If a horse is not very sensitive to flies or there are not many flies around, then it is not necessary to use a repellent at all. For a horse as sensitive as mine, Dr. Jones recommends looking more closely at the horse's environment and at the possibility of an allergy to gnats. Remove manure and drain standing water. Apply insecticides to the premises, if necessary. Once the source of flies has been minimized, then consider repellents.