Thyroid gland. Hashimoto's disease is a condition in which your immune system attacks your thyroid, a small gland at the base of your neck below your Adam's apple.The thyroid gland is part of your endocrine system, which produces hormones that coordinate many of your body's activities.ashimoto's disease is the most common cause of hypothyroidism in the United States. It primarily affects middle-aged women but also can occur in men and women of any age and in children. Doctors test your thyroid function to help detect Hashimoto's disease.