Eye color
Most horses typically have brown eyes. Some, however, will have a single or two blue or glass eyes.

Chestnuts
Chestnuts are hardened areas of skin on the horse''s legs that can be used as a fingerprint. Each chestnut has an individual design, and therefore is another method of equine identification.

Cowlicks or whorls
Cowlicks or whorls, otherwise known as trichoglyphs, are unique patterns, sizes, and combinations in a horse's hair. Not all horses have these, but the size, location, and direction of cowlicks or whorls are used by some breed associations. Cowlicks or whorls are most commonly located on the forehead, neck, and flank area. They are difficult to evaluate except when observed up close.

Scars and blemishes
Any permanent scars and/or blemishes that a horse has should be recorded and photographed for the horse owner's records.

Parentage Verification
There are two principal methods that are used to determine if a horse is an actual descendant of a particular sire and dam.

• Blood typing
  This method is exactly the same method used when blood typing humans using genetic blood group markers (the ABO and Rh system), along with electrophoretic methods (uses and electrical current to separate molecules according to their genetic makeup). The sire and dam of a certain blood type can only yield an offspring with a certain blood type. However, you must know the suspected parentage blood type in order to perform this test, and it is more of an elimination process rather than a confirmation. That is, it tells you who the horse's parents are not rather than who they are.
  
• DNA testing
  Although not available to everyone and very costly, DNA testing is the new technology for parentage verification that is currently becoming utilized by more and more breed registries. It is ideal for parentage verification and is a much more accurate method of determination when compared to blood typing. The benefit to DNA testing is that it doesn't require a blood sample. The test is commonly run from mane or tail hairs or a nasal swab, both of which are easy to acquire.

Hot Iron Branding or Fire Branding
This is one of the oldest methods of identification and is still utilized in certain areas. Hot branding uses an iron that is heated electrically or by fire to burn a brand into the hair follicles, resulting in permanent hair loss in that area. These types of brands are harder to observe when used on light-colored horses and when hair has grown over the brand.

Electronic Identification
The use of microchip implants in the identification of horses has been increasingly popular over the last decade. The invisible microchip is usually placed in the neck by a licensed veterinarian in a similar method to giving an injection. Once in place, a radio frequency scanner can be used to detect the microchip. Many horse owners prefer this method of identification because it does not change the outward appearance of the horse and at the same time allows for the same chance of recovery if the horse is stolen. However, it may not deter theft in the same manner that a brand would.

Lip Tattoos
Lip tattoos are pretty self-explanatory. They are a combination letter and number tattoo that is placed on the inside of the upper lip of a horse. The Jockey Club requires that all racing Thoroughbreds have lip tattoos as a verification procedure. Other breed associations have also adapted this identification method as a method of identification of an individual horse (racing, quarter horses, and standardbreds). Lip tattoos begin to wear after 4-5 years, and will continue to fade over time.