evidence: - Hashimoto's thyroiditis: In this autoimmune disorder, the body attacks thyroid tissue. The tissue eventually dies and stops producing hormones. [...] Alternative Treatment for Thyroid Problems [...] Protein, calcium, magnesium, and iodine help your thyroid work. Make sure you're getting plenty of all the B vitamins, vitamin A, and vitamin C. If you don't have enough iodine in your system, taking selenium can cause hypothyroidism.