The most common cause of scratching and rubbing in horses in allergies to flying insects, which should be much decreased in winter due to less insects. So if your horse scratches and rubs in the summer but seems much better in the winter, the scratching is likely related to a flying insect allergy. However, if your horse is still scratching in winter, there are multiple other causes, such as allergies to pollen or food. In most horses with atopy or inhalant allergies, it begins as seasonal allergies but may progress to year round problems.
Dr. Susan White from Georgia indicates in the Practitioner publication that atopy usually starts when the horse is less than 7 years old. These horses usually scratch the face, legs, neck, mane and tail. Food allergies can also occur but appear to be rare in horses. To diagnose a food allergy, limiting the diet to one type of forage for 4 weeks or longer may be required to make the diagnosis. Generally starting with grass hay is a good idea as alfalfa or peanut hay are more likely to be related to food allergy. Dr. White indicates that soy is a common ingredient in many commercial concentrate foods and is a common allergen. Sweet feeds or any feed with molasses is also a common allergen, so all of these feeds should be eliminated except grass hay, and then added in one by one to determine the offending feed. Although that sounds simple, it is not as diagnosing food allergies can be complicated. Other possible causes of itching in horses in the winter are biting and sucking lice, ringworm, bacterial infections, yeast infections or immune mediated disease so if your horse is itchy in winter, call your vet for an exam.