For most horses, the best equine wart remedy is simply tincture of time. Warts usually occur in young horses ages 4 and under, whose immune systems aren't completely mature, and disappear within nine months of their initial appearance. Caused by the papilloma virus, young horses can spread the virus to each other. Insect bites are another wart vector.
Your horse may experience a wart or two, or literally hundreds of them. Multiple warts may resemble little cauliflowers. Warts most often appear on the face, inner ears, legs and on the penis of male horses. They are primarily a cosmetic issue, unless there are so many they affect the animal's ability to eat or the placement of tack.
Because young horses can spread warts to one another, keep a horse full of warts separate from other young stock and don't share his grooming tools, tack or feed and water buckets with other equines.
Old Horsemen's Remedies
Horsemen pass various equine remedies down from generation to generation -- whether any of them actually work is another story. One old-fashioned wart remedy consists of crushing the warts, then feeding the crushed bits to the animal as a sort of primitive vaccine. There's no real evidence this method has any merit.
If your horse has warts, your vet can surgically remove them. There's some anecdotal evidence that surgical removal of a few warts in a horse loaded with them can speed the process at which the others disappear, but it's quite possible it was just time for the warts to cease existing.
Rarely, a wart develops a secondary infection if it is rubbed by tack or the horse scrapes it against something. In that case, the open lesion invites bacteria to enter. Larva also can invade the sore, resulting in "summer sores." A dose of the dewormers ivermectin or moxidectin generally will cure summer sores.