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I've had lower back pain as well since I started on synthroid. . .actually a bit before when I was on the PTU as well. . .I wasn't sure if it was from going Hypo or from the weight that I have put on as result of my treatment. . .I'm leaning toward the weight gain. . .
So sorry you are going through this. Just 2 cents as I was thinking I got awful pain in my lower back when a stone was "on the move".
C~
best of luck to you!