Most people with hyperthyroid (overactive) or hypothyroid (under-active) thyroid glands have "thyroid autoimmunity" as the cause. I'll first mention some basic things but will also add some not-too-often recognized facts on the close relationship of Hashimoto’s thyroiditis to Graves’ Disease following below.
When hypothyroidism occurs from antibodies attacking the gland, it is referred to as Hashimoto's thyroiditis. There are other types of thyroiditis that are very similar to Hashimoto's but are rare and doctors usually place them under the Hashimoto's umbrella if thy are chronic (ongoing/permanent types).
When hyperthyroidism occurs from antibodies attacking and attaching to the thyroid gland, it's called Graves' Disease.
Some patients have both diseases at the same time and when this happens as a temporary thing, they refer to it as Hashitoxicosis. Uncommonly it can be a permanent wavering back and forth between the two and when this happens even doctors are stumped as to whether it should be diagnosed in the Hashimoto's or Graves' category. It's not very common but I've received enough emails and seen enough posts by people on thyroid forums to know it does happen and I'm convinced it's not as rare (near non-existent) as was once believed.
A treatment that has been used in parts of Europe for a mixed thyroid disease as described above is something they call "block & replace therapy". They give these patients a regimen of an anti-thyroid drug, then after suppressing the thyroid for a time, will replace the low hormone for hypothyroidism it causes. This treatment is rare in the U.S. but may become more commonly used over time.
Other patients that are hard to regulate on a dose of thyroid replacement hormone for hypothyroidism are referred for a thyroidectomy (gland removal) or ablation (destruction of the gland by radioactive iodine). It's rare that doctors recommend these two treatments or the block & replace I described earlier for patients who phase between hyperthyroid and hypothyroid. Thyroid removal especially is usually only done with hyperthyroid patients who have Graves' Disease or nodules (tumors) that are causing problems or are suspicious of containing malignant cells.
This is my lay-opinion but I feel patients should ask their doctors to order "thyroid antibodies" and to make sure a test for the "TSI" (Thyroid Stimulating Imunnoglobulins) is included if they are having problems with phasing between hyperthyroid and hypothyroid. They will likely test positive for the ones typically found in both Hashimoto's & Graves' being the "TPO" (and possibly the "TG") antibodies. If they also test positive for the TSI ones, they might be diagnosed as having Hashitoxicosis (intermittent hyperthyroidism) or co-occurring Graves' Disease.
It's not unusual for it to take several trials of thyroid hormone doses in newly treated hypothyroid patients, by their doctors to see what works over time. This is also why it's so important to have a doctor who takes real interest in getting the treatment as adequate and even as optimized as possible.
If over time a patient's levels still fluctuate widely even while they're on a stable dose, their case may require another qualified Endocrinologist or thyroid specializing doctor for a second opinion. I always suggest this as fellow-patient opinion, especially if thyroid removal (thyroidectomy) or thyroid ablation (destruction by Radio Active Iodine) is recommended. Doctors usually only recommend these as last resorts but they are serious proceedures and the patient should be thoroughly informed if they are considered and reassured that they need to be done.
Some hypothyroid patients who have a rough start on hormone replacement therapy, end up leveling out fine later on and the right brand and dose can also make a difference in successful treatment.

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