Your doctor didn't mention the autoimmune aspect of thyroid disease because it doesn't affect conventional treatment. But it makes all the difference for natural treatment. To treat the thyroid, you must treat the immune system.

The most important test for thyroid is the blood test for thyroid antibodies. Thyroid antibodies can cause symptoms even when TSH is normal. In particular, they have been shown to have a role in fertility and miscarriage. ^(1,2)  (For more about thyroid testing, check out Lara's blog post: TSH Is Unreliable.)

Thyroid patients with high thyroid antibodies report more symptoms than patients with low thyroid antibodies, even if their thyroid function test is normal. In other words, thyroid replacement is not enough to ameliorate symptoms of autoimmune thyroid disease. ⁽⁵⁾  According to Dr Emerson (editor of the prestigious journal Thyroid):  

As long as thyroid antibodies remain high "... optimal doses of thyroid hormone will not completely ameliorate all symptoms" 

Thyroid extract (also called desiccated thyroid or Armour thyroid) is sometimes better treatment, but NOT because it's bioidentical

There has been a surge in popularity of thyroid extract (also called natural thyroid), and I think that a clarification is in order. Thyroid extract is desiccated thyroid gland from a pig. It has a long history of use in medicine, and 50 years ago, it was the standard in thyroid medication. Thyroid extract contains both T4 and T3, and therein lies it's advantage. As discussed below, many people feel better when they take both T4 and T3. But, the T4 in thyroid extract is EXACTLY the same hormone as the T4 in conventional thyroxine. Therefore, thyroid extract is no more bioidentical than conventional T4.

Thyroxine (standard T4) IS bioidentical. But it's not T3, so in many cases, it is not enough treatment. 

Standard T4 thyroid medication is often not enough

The addition of T3 medication is helpful for many thyroid patients. In a double-blind crossover study (considered the gold standard for medical research), Danish researchers found that the addition of T3 to conventional thyroxine (T4) treatment significantly improved patients' quality of life, and relieved depression. Study participants improved in mood, vitality, sensitivity, social functioning and general health. There were no side effects and the blood marker TSH was kept stable. ⁽⁷⁾

T3 can be taken as conventional T3, or in the form of desiccated thyroid, or thyroid extract (which contains T4 and T3). 

How do you know if you have a thyroid problem?

Symptoms of under-active thyroid include fatigue, depression, hair loss, fluid retention, menstrual problems, high cholesterol, and more.

Untreated thyroid disease leads to heart disease, muscle weakness, poor mental function, and an increased risk for cancer. Some experts believe that it may be responsible for 40% of unexplained cases of fatigue, depression, weight gain and infertility ⁽⁶⁾.

Suspect thyroid? A standard blood test may have missed it.

The standard test for TSH is out-dated and inaccurate

If you suspect low thyroid function but have had "normal" blood tests, you and your doctor may want to take a second look. A TSH of greater than 2.5 is not normal. 

More than a decade ago, the American National Academy of Clinical Biochemistry narrowed the reference range for thyroid stimulating hormone (TSH) from 0.5-5.0 to 0.2-2.5mIU/L.  Similar revisions by the American Association of Clinical Endocrinologists (AACE) meant that 13 million people previously considered to be normal, could now become officially diagnosed with under-active thyroid. ⁽³⁾

You should also consider the fact that TSH is lower if the blood test is taken later in the day, and if you ate before the test. ⁽⁴⁾ Other factors can cause an inaccurate TSH reading, such as a deficiency in the adrenal hormone cortisol. (For more about TSH, check out Lara's new blog post: TSH is Unreliable.)

What additional tests might you need?

If thyroid disease is suspected, blood tests should not be limited to TSH.  The most useful test is thyroid antibodies. Other useful tests include free T3, free T4, reverse T3, DHEA-s, serum vitamin D, salivary cortisol, gliadin IgG (gluten test) and urinary iodine.

What is reverse T3? 

To be effective, T4 needs to be converted to its active form T3 hormone. Most of this conversion happens in the liver and muscle tissue. The conversion will not occur when there is insulin resistance or inflammation, and T4 will instead be converted to an inactive hormone called reverse T3. After years on conventional thyroid treatment (T4), high levels of reverse T3 can accumulate. This effectively BLOCKS the thyroid receptors, and causes symptoms of under-active thyroid, even though the standard blood tests for TSH, T3 and T4 are normal.

Impaired conversion of T4 to T3 can also be caused by the elevation of the stress hormone cortisol.

Do you react with anxiety and heart palpitations when you take thyroid medication?

The most common explanation for this an underlying problem with adrenal insufficiency (cortisol and DHEA deficiency). Correct the adrenal problem, and then you should be able to tolerate thyroid medication.

Do you have low blood pressure?

Many women with Low Blood Pressure Syndrome also have autoimmune thyroid disease.

Thyroid disease could be WHY you have elevated cholesterol

Thyroid hormone is necessary for the healthy metabolism of cholesterol. Elevated cholesterol is possibly the single most common symptom of under-active thyroid. But most doctors and patients are unaware of this link. According to a survey conducted by the American Association of Clinical Endocrinologists, fewer than half of people diagnosed with high cholesterol had had their thyroid checked, and 90% of survey participants were unaware of the thyroid's impact on cholesterol. 

Common causes of thyroid problems

Why is thyroid disease so common?  Like many other hormone imbalances, under-active thyroid is due, in part, to our modern lifestyle.  Causes include:

• Autoimmune thyroiditis (Hashimoto's) is the most common reason for under-active thyroid. In this condition, the immune system attacks the thyroid gland, and it also as interferes with the action of thyroid hormone in the body. Thyroid hormone tablets are not adequate treatment. The immune problem must also be addressed. Thyroid autoimmunity affects 1 in 4 women. It is the result of environmental toxins and widespread vitamin D deficiency. It is also caused by wheat gluten, which has been shown to be a trigger for Hashimoto's⁽⁸⁾ (See Autoimmune article.)
• Selenium deficiency (a serious problem in Australia due to low soil levels).  Selenium is necessary for the conversion of T4 to T3.  (Incomplete conversion results in high levels of reverse T3, an inactive hormone.) Selenium has also been shown to reduce autoimmunity against the thyroid (ie. to treat the underlying cause of Hashimoto's thyroid disease.) ⁽⁹⁾ It also protects against the toxic effect of iodine on the thyroid.
• Oestrogen dominance caused by stress and pollution.  Oestrogen suppresses thyroid function.
• Environmental toxins affecting the thyroid gland, such as mercury ⁽¹⁰⁾, bromine, chlorine, fluoride, PCBs and others. According to new research presented at the American Thyroid Association meeting, "environmental factors account for about 30% of the risk for autoimmune thyroid disease". ⁽¹¹⁾ Of concern are certain pharmaceutical medications, cigarette smoking, stress, selenium deficiency, pesticides, polychlorinated biphenyls (PCBs), and bisphenol A (BPA).
• Adrenal insufficiency (or dysregulated HPA axis). A deficiency in the adrenal hormones DHEA or cortisol is a common underlying issue in thyroid disorders. If it is not corrected, patients may find that they cannot tolerate thyroid replacement treatment. Cortisol deficiency may suppress TSH. Read about Low Blood Pressure Syndrome for more information on adrenal insufficiency.
• Iodine deficiency. Deficiency is very common in Australia. Get your iodine level checked with a urine test, and then use a proper low-dose iodine supplement, not kelp. Kelp is not effective because it also contains bromine which inhibits thyroid function. Hashimoto's patients should use iodine with caution, as large doses may aggravate your condition. (Read Lara's iodine safety article.) If an iodine deficiency has been established with a urine test, then a small dose of iodine can be used, even by Hashimoto's patients. Iodine is not the solution for every thyroid problem, but a deficiency should be corrected. Iodine is not just about thyroid. It is important for the health of the brain, breasts, and uterus. And if an iodine deficiency is not corrected, then the body will harvest iodine from the thyroid hormone medication.
• Iron deficiency. The thyroid needs adequate iron to make thyroid hormone. 

Treatment of thyroid disease

You need to correct immune function. See Lara's article on autoimmune disease.

Effective strategies for addressing the autoimmune aspect of Thyroid disease include:

• Avoid wheat.
• Selenium to reduce autoimmunity.
• Correct vitamin D deficiency
• Improve gut flora
• Reduce stress
• Correct underlying adrenal issue, such as DHEA or cortisol imbalance.
• Correct oestrogen dominance. Consider using Natural progesterone.
• Detoxify mercury and other toxins. (Testing for mercury toxicity is available at Sensible-Alternative Clinic).
• Supplement selenium to lower thyroid antibodies. Also helps with conversion of T4 to T3.
• Correct an iron deficiency.
• Herbal medicine Bupleurum, Turmeric, Rehmannia and others.

Other Naturopathic treatments for thyroid.

• Herbal medicines Withania or Coleus to increase production of thyroid hormone. (See Best Herbs for Women article.)
• Iodine (not kelp) but in LOW dose. Use with caution in Hashimoto's disease.
• Amino acid tyrosine which is the building block for thyroid hormone.
• N-acetyl cysteine to detoxify
• Vitamin B6 and Vitamin A to improve the function of the thyroid gland.
• Selenium and zinc to ensure conversion of T4 to T3.
• Coconut milk/ coconut oil provides medium chain fatty acids to normalise gut flora and stimulate metabolic rate.
• Exercise
• Sleep
• Thyroid hormone supplements. See below.

Thyroid hormone supplements

Supplementation with thyroid hormone is the standard medical treatment for underactive thyroid.  Some hormone medication, however, is better than others.  This is because many people to not respond well to T4 (thyroxine) alone.  Thyroxine does normalise blood tests, but it cannot relieve low thyroid symptoms until is has been converted it to T3, the active hormone.  Failure to make this conversion is common.  (Selenium, zinc vitamin B6 and other co-factors are required.)

Two alternative prescriptions are available:

1. T3 (Standard T3 or the much preferred, but more expensive, slow-release T3) used together with T4 long term or by itself for a short-term correction.
2. Thyroid Extract (desiccated thyroid, Armour thyroid) is popular. It can be a good choice for non-autoimmune thyroid problems, or for Hashimoto's if the antibodies are not too high. High thyroid antibodies may be aggravated by thyroid extract. Thyroid extract is available by prescription from compounding chemists.  

References

(1) Stagnaro-Green A et al.. A prospective study of lymphocyte-initiated immunosuppression in normal pregnancy: evidence of a T-cell etiology for postpartum thyroid dysfunction. J Clin Endocrinol Metab 1992;74:645-653.

(2) Bussen, S et al. Increased prevalence of thyroid antibodies in euthyroid women with a history of recurrent in-vitro fertilization failure. Human Reproduction. 2000. 15(3): 545-548

(3) AACE Medical Guidelines for Clinical Practice for the Evaluation and Treatment of Hyperthyroidism and Hypothyroidism, Endocrine Practice, Vol.  8, No.  6, Nov/Dec 2002.

(4) Scobbo RR et al. TSH variability in normal individuals: the influence of time of sample collection. W V Med J. 2004;100:138-142

(5) Ott, J et al. Hashimoto's Thyroiditis Affects Symptom Load and Quality of Life Unrelated to Hypothyroidism: A Prospective Case-Control Study in Women Undergoing Thyroidectomy for Benign Goiter. Thyroid. 2011 Feb;21(2):161-7. PMID: 21186954

(6) Barnes, Broda.  Hypothyroidism: The Unsuspected Illness. 1976

(7) Nygaard, B et al. Effect of combination therapy with thyroxine (T4) and 3,5,3#-triiodothyronine versus T4 monotherapy in patients with hypothyroidism, a double-blind, randomised cross-over study. 2009. Euro Journal of Endocrinology. 161(6): 895–902. PMID: 19666698

(8) Sategna-Guidetti C et al. Prevalence of thyroid disorders in untreated adult celiac disease patients and effect of gluten withdrawal: an Italian multicenter study. Am J Gastroenterol. 200. ;96(3):751-7.

(9) Mazokopakis EE, et. al. Effects of 12 Months Treatment with l-Selenomethionine on Serum Anti-TPO Levels in Patients with Hashimoto's Thyroiditis. Thyroid. 2007 Aug;17(7):609-12

(10) Barregard L, Lindtedt G, Shutz A, et al.  Endocrine function in mercury exposed chloralkali owkers.  Occup Environ Med 1994, 51 (8)536-540

(11) Medscape Medical News from the American Thyroid Association (ATA) Spring 2010 Meeting. Presented May 15, 2010

(12) Manson JE, et al. New findings from the Kronos early estrogen prevention study (keeps) Randomized trial.  NAMS 2012. 23rd Annual Meeting. Presented October 3, 2012.