Hashimoto's Disease causes inflammation of your thyroid. It is an autoimmune disorder in which your immune system inappropriately attacks your thyroid gland, causing damage to your thyroid cells and upsetting the balance of chemical reactions in your body. The inflammation caused by HD, also known as chronic lymphocytic thyroiditis, often leads to an underactive thyroid gland (hypothyroidism).  Hashimoto's disease is the most common cause of hypothyroidism.
Doctors use blood tests of thyroid function to detect Hashimoto's disease. Treatment of Hashimoto's disease with thyroid hormone replacement medication usually is simple and effective.
Hashimoto's disease does not have unique signs and symptoms. The disease typically progresses slowly over a number of years and causes chronic thyroid damage, leading to a drop in thyroid hormone levels in your blood. The signs and symptoms, if any, are those of an underactive thyroid gland (hypothyroidism).
The signs and symptoms of hypothyroidism vary widely, depending on the severity of hormone deficiency. At first, you may barely notice any symptoms, such as fatigue and sluggishness, or you may simply attribute them to getting older.                                                         
As the disease progresses, you may develop more obvious signs and symptoms, including:
Increased sensitivity to cold
Pale, dry skin
A puffy face
Hoarse voice
An elevated blood cholesterol level
Unexplained weight gain — occurring infrequently and rarely more than 10 to 20 pounds, most of which is fluid
Muscle aches, tenderness and stiffness, especially in your shoulders and hips
Pain and stiffness in your joints and swelling in your knees or the small joints in your hands and feet
Muscle weakness, especially in your lower extremities
Excessive or prolonged menstrual bleeding (menorrhagia)
Without treatment, signs and symptoms gradually become more severe and your thyroid gland may become enlarged (goiter). In addition, you may become more forgetful, your thought processes may slow, or you may feel depressed.
Your thyroid gland produces two main hormones, thyroxine (T-4) and triiodothyronine (T-3). They maintain the rate at which your body uses fats and carbohydrates, help control your body temperature, influence your heart rate and help regulate the production of protein.
The rate at which thyroxine and triiodothyronine are released is controlled by your pituitary gland and your hypothalamus — an area at the base of your brain that acts as a thermostat for your whole system. The hypothalamus signals your pituitary gland to make a hormone called thyroid-stimulating hormone (TSH). Your pituitary gland then releases TSH — the amount depends on how much thyroxine and triiodothyronine are in your blood. Finally, your thyroid gland regulates its production of hormones based on the amount of TSH it receives. Although this process usually works well, the thyroid sometimes fails to produce enough hormones.
Your immune system's role
Normally, your immune system uses naturally occurring proteins (antibodies) and white blood cells (lymphocytes) to help protect against viruses, bacteria and foreign substances (antigens) that invade your body. Hashimoto's disease is an autoimmune disorder in which your immune system creates antibodies that damage your thyroid gland. The disease causes inflammation of your thyroid gland (thyroiditis), which may impair the ability of your thyroid to produce hormones, leading to an underactive thyroid gland (hypothyroidism). Then, your pituitary gland attempts to stimulate your thyroid gland to produce more thyroid hormones, thus causing your thyroid gland to enlarge (goiter).
Doctors don't know what causes your immune system to attack your thyroid gland. Some scientists think a virus or bacterium might trigger the response, while others believe a genetic flaw may be involved. Most likely, Hashimoto's disease results from more than one factor. A combination of factors, including heredity, sex and age, may determine your likelihood of developing the disorder. Hashimoto's disease is most common in middle-aged women and tends to run in families.
When to seek medical advice
See your doctor if you're feeling tired for no apparent reason or have any other signs and symptoms of hypothyroidism, such as dry skin, a pale, puffy face, constipation or a hoarse voice.
You'll also need to see your doctor for periodic testing of your thyroid function if you've had previous thyroid surgery, treatment with radioactive iodine or anti-thyroid medications, or radiation therapy to your head, neck or upper chest.
If you have high blood cholesterol, talk to your doctor about whether hypothyroidism may be a cause. And if you're receiving hormone therapy for hypothyroidism caused by Hashimoto's disease, schedule follow-up visits as often as your doctor recommends. Initially, it's important to make sure you're receiving the correct dose of medicine. And over time, the dose you need to adequately replace your thyroid function may change.
Tests and diagnosis
In general, your doctor may test for Hashimoto's disease if you're feeling increasingly tired or sluggish, have dry skin, constipation and a hoarse voice, or have had previous thyroid problems or goiter.
Diagnosis of Hashimoto's disease is based on your signs and symptoms and the results of blood tests that measure levels of thyroid hormone and thyroid-stimulating hormone (TSH). These may include:
A hormone test
Blood tests can determine the amount of hormones produced by your thyroid and pituitary glands. If your thyroid is underactive, the level of thyroid hormone is low. At the same time, the level of TSH is elevated because your pituitary gland tries to stimulate your thyroid gland to produce more thyroid hormone.
An antibody test
Because Hashimoto's disease is an autoimmune disorder, the cause involves production of abnormal antibodies. A blood test may confirm the presence of such antibodies.
In the past, doctors were unable to detect underactive thyroid (hypothyroidism), the main indicator of Hashimoto's disease, until signs and symptoms were fairly advanced. But by using the sensitive TSH test, doctors are able to diagnose thyroid disorders much earlier, often before you experience any signs and symptoms. Because the TSH test is the best screening test, your doctor will likely check TSH first and follow with a thyroid hormone test if needed. TSH tests also play an important role in managing hypothyroidism. These tests also help your doctor determine the right dosage of medication, both initially and over time.
Left untreated, an underactive thyroid gland (hypothyroidism) caused by Hashimoto's disease can lead to a number of health problems:
Constant stimulation of your thyroid to release more hormones may cause the gland to become enlarged, a condition known as goiter. Hypothyroidism is one of the most common causes of goiter. Although generally not uncomfortable, a large goiter can affect your appearance and may interfere with swallowing or breathing.
Heart problems.
Hashimoto's disease also may be associated with an increased risk of heart disease, primarily because high levels of low-density lipoprotein (LDL) cholesterol — the "bad" cholesterol — can occur in people with an underactive thyroid gland (hypothyroidism). Hypothyroidism caused by Hashimoto's disease also can lead to an enlarged heart and, in rare cases, heart failure.
Mental health issues.
Depression may occur early in Hashimoto's disease and may become more severe over time. Hashimoto's disease can also cause sexual desire (libido) to decrease in both men and women and can lead to slowed mental functioning.
This rare, life-threatening condition can develop due to long-term hypothyroidism as a result of untreated Hashimoto's disease. Its signs and symptoms include intense cold intolerance and drowsiness followed by profound lethargy and unconsciousness. A myxedema coma may be triggered by sedatives, infection or other stress on your body. Myxedema requires immediate emergency medical treatment.
Birth defects.
Babies born to women with untreated Hashimoto's disease may have a higher risk of birth defects than may babies born to healthy mothers. Doctors have long known that these children are more prone to intellectual and developmental problems. There may be a link between hypothyroid pregnancies and birth defects, such as cleft palate. A connection also exists between hypothyroid pregnancies and heart, brain and kidney problems in infants. However, if any of these conditions are diagnosed within the first few months of a baby's life, chances of normal development are excellent.

Treatments and drugs
Treatment for Hashimoto's disease may include observation and use of medications. If there's no evidence of hormone deficiency and your thyroid is functioning normally, your doctor may suggest a wait-and-see approach.
Replacement hormones
If Hashimoto's disease causes thyroid hormone deficiency, you may need replacement therapy with thyroid hormone. This usually involves daily use of either a  synthetic thyroid hormone levothyroxine (Levothroid, Levoxyl, Synthroid) or a natural porcine extract. Synthetic levothyroxine is identical to thyroxine - T4, the natural version of this hormone made by your thyroid gland.   These products ( Armour Thyroid or Naturethroid - available in New Zealand under the name Whole Thyroid Extract), for example — contain both levothyroxine and triiodothyronine (T3), as well as traces of T2, T1, T0 & Calcitonin.  The oral medication restores adequate hormone levels, returning your body to its normal functioning.                                                                 
Soon after starting treatment, you'll notice that you're feeling less fatigued. The medication also gradually lowers cholesterol levels elevated by the disease and may reverse any weight gain. Treatment with levothyroxine is usually lifelong, but because the dosage you need may change, your doctor is likely to check your TSH level every six to 12 months.
Monitoring the dosage
To determine the right dosage of medication, your doctor should check your levels of TSH, Ft3 & Ft4 after a month or two. Excessive amounts of TSH can accelerate bone loss, which may make osteoporosis worse or add to your risk of this disease. Overtreatment with levothyroxine/WTE also can cause heart rhythm disorders (arrhythmias).
If you have coronary artery disease or severe hypothyroidism, your doctor may start treatment with a smaller amount of medication and gradually increase the dosage. Progressive hormone replacement allows your heart to adjust to the increase in metabolism.
Levothyroxine/WTE causes virtually no side effects when used in the appropriate dose. If you change brands, let your doctor know to ensure you're still receiving the right dosage. Also, don't skip doses or stop taking the drug because you're feeling better. If you do, signs and symptoms will gradually return.

Could Antibiotics Cure Your Hashimoto's Disease? Read this article by Mary Shomon

Effects of other substances
Certain medications, supplements and even some foods may affect your ability to absorb thyroid hormones.  Talk to your doctor if you eat large amounts of soy products or a high-fiber diet, or if you take any of the following:
Iron supplements incl. multivitamins that contain iron - 4 hrs before or after medication  
Cholestyramine (Questran), a medication used to lower blood cholesterol levels
Aluminum hydroxide, which is found in some antacids
Sodium polystyrene sulfonate (Kayexalate), used to prevent high blood potassium levels
Sucralfate, an ulcer medication
Calcium supplements   -  at least 1 hr before of after medication