What is headshaking?
Headshaking is a mysterious problem in horses.  Recent research suggests that it can be caused by a variety of factors:  it can be behavioral (a vice or disobedience) or biological (caused by physical discomfort arising from tack, teeth or ear problems, allergies, nerve stimulation, sensitivity to light, and a variety of other possible causes). 

The symptoms of headshaking are snorting, sneezing, and pronounced shaking of the head characterized by a side-to-side or vertical "snatching" motion, as though the horse had an insect up its nose.  Headshaking horses will often try to scratch their noses on their legs, on posts, or on the ground.  Headshaking tends to occur when horses are stressed by exercise or other factors.  Most important, it tends to be seasonal, triggered in the spring or early summer, and tends to subside in winter.

Scientists posit that headshaking may be triggered by strong light (photic headshaking), which stimulates the fifth cranial nerve, called the trigeminal nerve, in the horse's face and causes uncontrollable itching, pain, and/or sneeziness.  (Interestingly, this phenomenon affects as many as 25% of humans as well, and is called the photic sneeze or "ACHOU syndrome.")  Photic sneezing is hereditary in humans and may also be in horses.  Some humans also suffer from an irritation of the trigeminal nerve called trigeminal neuralgia (TgN) that can cause facial pain and muscle paralysis.  The genesis of TgN, which primarily affects women over 50, is still being investigated by neurologists; these studies may indirectly help us understand photic headshaking in horses.

Recent studies suggest, but do not prove, that headshaking may possibly be triggered by rhinopneumonitis vaccinations, which may activate the herpes virus (EHV-1, EHV-4) which lies dormant in the horse's trigeminal nerve.  This process is roughly analogous to the onset of shingles in humans. 

Headshaking in horses is poorly understood, and just beginning to be systematically researched.  It may have multiple causes rather than a single cause.  We do know that horses tend to begin to headshake at maturity.  Some horses headshake all the time, while others headshake only when under saddle or in strenuous exercise.  Sometimes headshaking resolves spontaneously.