Yes, there are quite a few medical conditions that can cause a horse to throw his head. Some of them are insect irritation, vision or eye irritations, allergies, ear or head pain, oral problems, or neurologic problems. When the horse is exhibiting the behavior only when a rider is on its back, the most likely cause of it is pain. This could be dental pain or even back pain. In such a case, make sure to visit the vet for better advice.