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In this article from the National Institutes of Health/National Library of Medicine website (PubMed), "rheumatic Manifestations" (joint & muscle pain) in relation to Hashimoto's thyroiditis (common cause of hypothyroidism) is addressed. The article is entitled; "Chronic autoimmune thyroiditis and rheumatic manifestations”. Here we have a medical reseach article that attributes this symptom problem to the underlying autoimmune disease and not to hormone levels only. In other words a treated hypothyroid patient can achieve a euthroid state (normalized thyroid hormone levels) but can potentially still experience rheumatic symptoms from the underlying thyroid autoimmunity. The important point this articles makes, is the fact that correcting hypothyroidism, in some patients, will not always resolve their joint and muscle aches completely.
Doctors who accuse treated hypothyroid patients of imagining (psychosomatic) their unrelieved symptoms, need to read this article.

The link>>
http://www.ncbi.nlm.nih.gov/pubmed/15288851