The most common cause for hypothyroidism is the autoimmune disease called Hashimoto's Thyroiditis, but some doctors don't really care about the cause -- including my former pcp. He never tested anything beyond TSH and FT4. If it had not been for my ENT, I would never have been tested for antibodies, nor had an ultra sound to find that I have nodules and a goiter.
To test for Hashimoto's you should have antibody testing (thyroid peroxidase antibodies, TPOab and Thyroglobulin antibodies, TGab). You should also have an ultra sound to check for goiter (enlargement) and nodules.
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