This may have been posted before but I found this an interesting link on coeliac disease/IBS and the connection between other autoimmune diseases, including thyroid disease:
thinkcoeliac.co.uk/expert-o...
Dr Saleem is the only one to mention that it can cause B12 deficiency.
The health of our gut has to be the focus for long term good health. I was diagnosed with Crohns over 40 years ago - Hashimotos ....just 9 years ago. Yes B12 deficient too ! Have been gluten free for over a year but anti-bodies only slightly reduced in that time 
Am remaining GF as something tells me intuitively - that it is right for me.
Healing the gut is a long term project - there are no quick fixes....
Yes, so agree about intuition and the gut feeling! Hope the antibodies go down in time Marz.
I kept reading about GF on these sites but was lazy about trying it even though I'd had IBS, gastritis, etc. for a number of years. I avoided cakes, biscuits, sugar etc. but found it hard to give up bread altogether. Having avoided gluten altogether for a few months, I find bloating, heartburn, etc has gone and I have more energy but, when I do transgress the symptoms come back with a vengeance, so I wonder if your body builds up some sort of tolerance over the years.
I hadn't realised how much it affected thyroid and that the other vague symptoms were B12 deficiency until researching for my relative.....more and more connections....
Menstrual Migraines and Thyroid Disease connection?Are thyroid anti bodies always high with coeliac disease? 
Is Interstitial Cystitis linked to Autoimmune thyroid disease? 
Is thyroid disease classed as an autoimmune disease?
Autoimmune thyroid disease (Hashimotos) but no inflammation - feel like an anomaly 
