For most patients who are diagnosed with hypothyroidism, the cause is an immune system dysfunction called “thyroid autoimmunity”, meaning the immune system has turned against the thyroid gland and is sending auto-antibodies (cells that normally destroy germs and allergens), to destroy it. The name for the resulting damage and inflammation in the gland is “Hashimoto’s thyroiditis” and a common medical term for the condition is “Chronic Lymphocytic thyroiditis”. There is however a non-immune related type of hypothyroidism, that is less common, called “Central Hypothyroidism”.

With Central Hypothyroidism, the low functioning thyroid gland (hypothyroidism) is a result of inadequate communication between the, system of endocrine glands, that work together in regulating thyroid function. The hypothalamus and pituitary glands are located in the brain and are the endocrine glands that send signals via hormones, to other glands in the body, including the adrenals and the thyroid. The hypothalamus is the first gland in the chain of command and sends a hormone to the pituitary gland, to signal it to release a hormone of its own that will afterward be sent to the thyroid gland, to regulate thyroid hormone production. TRH; “Thyrotropin Releasing Hormone” is the hormone the hypothalamus sends to the pituitary gland, to stimulate it to release a thyroid regulating hormone called TSH “Thyroid Stimulating Hormone”. Some medical sources call this the “hypothalamus-pituitary-thyroid axis”.

When something goes wrong within this system of glands whose end-purpose is regulating thyroid function, it can cause the thyroid to release inadequate amounts of hormone, resulting in hypothyroidism. If there is disease present in one of the two major brain glands (hypothalamus or pituitary), such as a tumor-adenoma that develops in one of them or damage occurs to them from traumatic injury they may fail to regulate the endocrine glands they are in charge of. A treating physician that diagnosis hypothyroidism in a patient, can determine the cause as being dysfunction in one of these glands, by blood testing the patient’s levels of TRH and TSH and/or by ordering brain imaging tests such as an MRI, that checks for the presence of tumors.

When a type of hypothyroidism, is not a problem within the thyroid gland itself, it is sometimes referred to as "Secondary Hypothyroidism". Central Hypothyroidism may sometimes be considered a secondary cause. When the thyroid gland is the cause due to a disease, injury or tumors/nodules affecting it, the term "Primary Hypothyroidism" is used.

Most patients who are diagnosed with Central Hypothyroidism are first suspected of having it, when their thyroid hormones (T-4 and/or T-3) are found to be at hypothyroid levels but the TSH level is in normal range or flagged low. A Low TSH usually indicates hyperthyroidism and not hypothyroidism and is why Central Hypothyroidism is investigated as a possible cause in these cases.