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Thyroid UK
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I had come to see if I could get an ultrasound referral about the lump and problems swallowing. My GP thinks I have acid reflux because of the problems swallowing and the lump in my neck and she's put me on omeprazole as well as paracetamol for the neck pain (which has gone away after I took one paracetamol tablet this morning)

She asked me about any symptoms relating to digestion/stomach problems and I told her even though I didn't think they were anything to worry about and would clear up on their own over time. I have loss of appetite, weight loss even though I eat three meals a day including breakfast and change of bowel movements (not watery but looser than they used to be and I've been used to being constipated for about 4 years now). I had a bad episode of heartburn about 6 years ago and put a lot of time and effort in getting the Gaviscon to work. Although it was one episode of reflux/heartburn I thought that would be the end of it but the symptoms I have now are not what I had when I had the reflux/heartburn the first time. So could my GP be right? She wants me to try the omeprazole but she's said if it doesn't work she'll refer me to an ENT.

I've looked on the net at how Hashimoto's can cause low acid problems which can lead to acid reflux and omeprazole lowers acid even further. Is that correct? If so should I not be taking it even though I've been prescribed it? Thank you :)

37 Replies

I'm no expert personally, but my aunt was put on omeprazole which I believe is classed as a proton-pump inhibitor. It exaserbated (sp?) her condition because it lines the stomach and restricts the digestive system with absorbing vits, minerals and her thyroxine. I'm sure more experienced and knowledgeable people will comment, but personally I wouldn't ever take omeprazole - particularly if you are on thyroxine and don't have acid reflux symptoms. I would be pushing for an ultrasound scan to diagnose - not just treat symptoms. I too have a lump sensation in my throat for three months, but no pain. I can't feel or see the lump externally, but it feels like something is stuck in my throat. My GP thinks it's related to sinuses. I disagree and want an ultrasound. If it was a lump in my breast, they'd send me for a scan! Hopefully someone else will comment - but it seems you are not confident in your GPs assessment. Good luck x

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Thanks! No, I'm not confident in my GP's assessment at all. I'm tempted to change practices.


I think your statement is correct. Personally, I think the sphincter is loose and allows acid to enter the esophagus rather than an abundance of acid. I didn't find that the inhibitors worked. Zantac seems to be a little more effective for me. Did you have an H. Pylori test?

There was something I remember I think called carafate. I'm not sure I even spelled that correctly but it would coat the acid and provide a barrier. Perhaps that is the same process as Gaviscon. I should check that out.


Hi, no I haven't been tested for H.Pylori. How can I get checked for that?

I'll look at the carafate. Thanks for suggesting that. :)


Hi Ella,

Thanks for putting some of your thyroid history in your Profile. It was helpful. It's not unusual to have swallowing problems with hypo but the lump on your neck should be checked by an Endocrinologist.

When hypothyroid it is quite possible that you have low acid rather than high, although the symptoms are similar - as you state above.

This is a link:


I was given something similar to Omeprazole and I was worse and in more pain than ever. Switched to Betaine plus Pepsin or Apple Cider Vinegar in juice or water, before or after meals, particularly protein and have had no problems since.

Get a new thyroid gland blood test and get a copy of the results with the ranges and post for comments. If you have pain, you may well not be on an adequate dose and the addition of some T3 may be helpful. She is treating your symptom (pain with paracetamol) instead of upping your dose of thyroid hormones. If she hasn't checked your B12, Vit D, iron, ferritin and folate ask for these to be done too. Don't take levo before your blood test, have test as early as possible and take meds afterwards. Paracetamol may be helpful in the meantime. Always take supplements 4 hours apart from thyroid medication. This is a link which is self-explanatory if you want to order any supplements:-



Thanks for links and suggesting the apple cider. I'll look at them in a sec and the apple cider sounds rather pleasant! :D

Here are my blood test results:

Thyroid Stimulating Hormone - 0.62 (0.2-4.2)

Anti-Thyroid Peroxidase Antibodies - 245 (<34)

Anti-Thyroglobulin Antibodies - 99 (0-115)

Ferritin - 28 (30-400) GP has put normal - no action

Do these look okay?

Folate, Vitamin D and B12 haven't been done recently. The latest results for those were done in May and I didn't register the importance of these results for thyroid:

Folate - 4.7 (4.1-18.7)

Vitamin D - 73 (50-75)

Vitamin B12 - 359 (180-900)


I guess the vitamin D MAY be all right but:

Ferritin - 28 (30-400) GP has put normal - no action


FERRITIN test: Measures your levels of storage iron, which can be chronically low in hypothyroid patients. If your Ferritin result is less than 50, your levels are too low and can be causing problems…as well as leading you into anemia as you fall lower, which will give you symptoms similar to hypo, such as depression, achiness, fatigue. If you are lower than the 50′s, you are scooting by. Optimally, females shoot for 70-90 at the minimum (Janie’s is 80 when her iron is good); men tend to be above 100 and optimally close to the 130′s. If your ferritin is much higher, you have INFLAMMATION–the latter causes iron to be thrust into storage and inflammation is common with thyroid patients for a variety of reasons. In less common cases, higher ferritin can be from liver disease, alcoholism, diabetes, asthma, or some types of cancer. Men are generally higher than women without having the above problems. If ferritin is high along with a high % Sat and Serum iron, you may have hemachromatosis or a MTHFR defect. Having heavy metals can push your ferritin low. You should be off all iron for at least 12 hours before testing to see what your body is hanging onto, and 5 days to see your true iron levels.

FOLATE test: Also called folic acid, this is a b-vitamin which can be low in hypothyroid patients. Folate is important for prenatal development, as well as your blood cell health. Folate works with B12 in the use and creation of proteins.


Thanks. :) So when I am next due for a ferritin retest (which won't be soon because the GP says I am "normal") - I will need to skip my dose of iron for at least 12 hours as well as 5 days?

Folate was done along with the Vitamin D and B12 were done in May. 4.7 (4.1-18.7). The GP says fine but it looks low to me.


I would say, yes. But I would look into foods that supply both. Folic acid is a synthetic form of folate and I've read many negative comments about taking it. Maybe a short term with nothing over 400 mgs. may be acceptable folic acid. Google it and see.

My ferritin is actually over the high range and it may be due to the things mentioned in the article but I also took a lot of ascorbic acid which binds to iron and keeps it circulating longer. That's why they say to take iron supplements with orange juice or vitamin C. It actually seems to be a long process to raise iron stores. My MIL was not absorbing iron at all and had to take injections of iron every day for 18 days.

It is especially important to have good levels because it insures that your T4 will convert to T3 which you absolutely must have in order to avoid symptoms of hypo.


Thanks. I think my local Wilko stocks folate tablets (I think, cannot be sure) but I can try to up my folate with foods instead. I have made some effort by eating eggs and salmon which I've just Googled are high in folate.

By the way I spoke to my GP about my symptoms as my medication review is due - she thinks my symptoms are not caused by hypothyroidism but something else. She hasn't said what the other causes are, though.


Ella, I've posted so many of Dr. Clark's videos which I believe are spot on regarding autoimmunity. It makes sense that the target of the attacks can be any specific part of the thyroid process. Sorry if I am repeating myself with you as I can't remember who has seen them, and also, he has 22 reasons for low thyroid so perhaps your GP is correct that it is not specifically your thyroid that is not functioning.

Be a detective.

Since you have TPO antibodies:

Low stomach acid:


Thank you Heloise for the video clips. If only all doctors were like this guy!

Regarding Anti-Thyroid Peroxidase Antibody levels: nobody in my family has Hashimotos. The only autoimmune illness in my family is diabetes but it's bypassed me. The only stress I might have experienced (major stress) is that I went through an operation about 3 years ago and I remember shaking like mad in the bed because they were going to put me out - which I never had done before. Maybe that might have turned the Hashimoto's on? Once you have the antibodies does any more testing need to be done to check the levels or is one test for antibodies enough?

Low stomach acid - I think the GPs now think I have malabsorption. Would a gastro find that? I now have apple cider vinegar that Shaws helpfully recommended, too. Dr Clark mentions side-effects of Rheumatoid Arthritis (which has interested me because I get joint pain) but if I tested negative for Rheumatoid Factor does that mean that they are not side effects of Rheumatoid Arthritis? Can I have testing for cytokines?

I think the GPs are thinking about putting me on anti-depressants as he mentions in the third clip because my GP I saw today wants me to make "more of an effort to get back to work". I am signed off with fatigue for now. I'll have to look at the other things he has mentioned - gut dysbiosis/leaky gut/food sensitivities. I'll have to Google these (if it's worth it!) and see what I find.


I do believe surgery is extreme stress to the body. I think adrenal function takes the hit when it comes to that and also the hypothalamus where stress is stored. Relaxation techniqus to release stored stress is a whole other subject. This is possibly the basis for ALL disease. Leaky gut is another kind of stress to your body as it fouls up your immune system. Antibiotics are a huge cause for gut dysbiosis. Gluten free seems to help. I try to limit carbs anyway.

I think the vinegar is worth a try and fights candida but so does nystatin if you have that problem. I'm not sure about these questions, my education has come from following medical websites (mostly alternative) for fifteen years (since I bought a computer). I am pretty sure that kind of doctor would be able to help with those kinds of questions. Cytokines was new to me and Dr. Clark has this:

When I was first ill and had so much body pain, they sent me to a rheumatologist and my RA factor was also negative so I don't know how much information you can gain from that. Usually the sedimentation rate shows when something is wrong and for inflammation the c-reactive protein (CRP) test indicates that.

My treatment was so poor in the beginning, I didn't even know about antibodies and was never told about them so I presume they never tested for them. Antibodies only tell you that you have had an attack. Usually it doesn't change the treatment although selenium is used as well as thyroid hormone to reduce them.

A short term of antidepressants might be all right.

I'd love to know all the answers, too, so keep learning!

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CRP test was normal I think. I didn't think to include that with the ferritin, folate, Vitamin D and Vitamin B12. It was below 1 (<5.00)

Would an alternative doctor be able to help? There is an NHS homeopathic hospital near me but I don't want the GP to think I'm going against their advice.

My antibodies doubled after I went gluten-free. :(


Really, about the gluten? What did you substitute for it? That is unusual....unless....the bit of iodine you may have been obtaining from yeast breads was depleted. I think in Europe much of the bread is unbromated. Do you notice that?

Try to stick with whole foods, your gut will like that, instead of having to figure out what to do with artificial ingredients.

I have such a suspicion of all doctors, I really don't know if you could find a good one and risk losing your coverage of the NHS.

You can get supplements on your own and you can optimize your immune system yourself. It's really more about what you do so you do have control over your health.


I substituted gluten and wheat for the shop-bought gluten free products. So things like pasta, cakes, bread, biscuits and chocolate were all shop-bought from the free from aisle.

Is there iodine in yeast?

Is it a good idea to look at supplements for every single vitamin and mineral? If my ferritin is low could that mean that my Vitamin C is low (since iron needs to be taken with Vitamin C)?

I've just noticed that one multivitamin I have contains iodine so is that one I should not be taking?


Before I forget, the GP did a coeliac blood test months ago but the time between when it was ordered to the time it was done was 2 weeks.

Is it possible that I need to leave more time for something to show up?


It's too long to go into but sometimes people are iodine deficient and that's why their thyroid isn't working. Once you have Hashimoto, they suggest you stay away from iodine but I think if you don't have it, it might be a good idea to include a small amount.

Bromides are bad and they started putting it in bread. That's why I asked you about it.

It's hard for me to tell you what to do. I don't know the whole story but there are some very excellent websites which you can search. I think we don't absorb the right nutrients so I think trying to get your gut straight might be a better way to go about this although I think a few supplements like magnesium glycinate, omega 3 and vitamin C are worth taking.




Thanks, I'll take a look. :)


Thanks for posting that, Shaws. It's one that escaped my notice. The undigested food actually causing the reflux makes sense. Dr. Stoll, a website I followed for years, suggested juicing a ginger root and taking a teaspoon of it every morning for a couple of weeks before breakfast for acid reflux. Unfortunately my juicer is broken.


I am sorry your juicer is broken. I like to grate a little ginger root into orange juice. I also like chocolate gingers.


HI I have had it for years, prescribed by gastro.I have had no bad affects at all especially not thyroid.



Okay. Thanks. Two people I know have been prescribed it - one of which is hypothyroid. I might try the apple cider idea Shaws suggested. :)

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Apple cider is quite strong, so take one or two teaspoons to start and dilute it either with water or juice. I swallow mine in one go when in water. You can take it before a meal or after.


Thanks, I'll consider this. It sounds quite sweet to me but it obviously isn't. :D


It is vinegar made from cider apples and many people quite like it.You can also use it in cooking. As mentioned some add it to fruit juice. It does settle my stomach and helps provides the acid which dissolves the protein we eat.

A link:


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Thank you Shaws for the link. The article also mentions Chamomile tea - I drink that in the evenings to help me sleep. Within seconds of drinking it my eyelids get heavy. :) I didn't know that could help with stomach acidity too!

I think Tesco sells apple cider vinegar as well but maybe it's better to make my own as then I know what's in it. :D


HI Good idea. If you take the drug have first thing am the full dose before anything else.



Hi well, I haven't yet picked up the Omeprazole because I started doing the Google searches and finding out that I most likely have low stomach acid and then when I realised what I've been given is for low stomach acid and might make my symptoms worse I haven't yet collected it.

Did you mean the Omeprazole first thing in the morning or the thyroid meds?


Hi First thing in the morning before anything. It is usually given for reflux or GORD.



Thanks Jackie! :)


Hi Ella78

I've had similar problems recently, indigestion for 3 months which coincided with finally being diagnosed as hypothyroid and crazy TSH levels. I took omeprazole for a month this summer and it was awful I had to stop taking it as it made the problems worse. So now I'm back to square one! I think there may be some truth in the low stomach acid idea, so hopefully apple cider will work for you before you have to resort to PPI meds. There's some usual info on the Chris Kresser website about indigestion and low stomach acid too. Good luck :-)


Thanks! I'll take a look. :) Sorry that the Omeprazole didn't work for you and I hope you get it sorted soon.


'They' gave it to me last year, when I was ill. I have no idea why, I've never had stomach/digesting problems.

When I was well enough to Google, I took myself off the horrible stuff! It had made me so ill.

I then found out that it had depleted my B12 and magnesium to levels bound to make me ill. Since then, I've had trouble getting the levels up.

I certainly wouldn't take it again, Under any circumstances!

Hugs, Grey

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I've taken omeprazole, plus lots of other remedies to neutralise or suppress stomach acid. None of them made me feel well. So now I am treating myself for low stomach acid and it is working better than anything I have ever taken for my gut problems before.

I am currently taking the following :

1) Probiotics twice a day. I don't stick to the same brand, instead I change it regularly to maximise the chances of me getting some benefit from lots of different good bacteria. I buy the best quality I can afford. I try to avoid taking the capsules with hot food or drink to reduce the chance of the bacteria getting killed off by heat. I take my second capsule last thing at night with plain water to give the bacteria a chance to populate my gut without any interference from stomach acid or anything else. My precautions may be based on dodgy logic - I really don't know. But my gut is feeling more comfortable than it has done for many years.

2) Betaine hydrochloride with every meal and every snack. I am currently taking Solgar betaine hydrochloride + pepsin tablets. I've also tried Biocare betaine hydrochloride + pepsin capsules. I can't tolerate the Biocare capsules, but the Solgar tablets work brilliantly. I had to experiment with timing (do I take them before, during first quarter/third of the meal, mid-way through, after 3/4 or 2/3 of the meal or after the meal?), and dosage. I'm taking one tablet about 1/3 of the way through a meal and a second about 2/3 of the way through a meal. It took a while for my inflammation and stomach irritation to subside, but now I only get very mild indigestion at bedtime - I'm still working on this...

3) Digestive enzymes with every meal. I'm currently taking Quest Enzyme Digest pills. I take one pill with each of the betaine hydrochloride + pepsin pills I take. I've tried some digestive enzymes by Zygest but they really didn't help me.

One thing that might happen - I got diarrhoea when I started taking each of these things (they were all started at different times), but in each case it wore off after 2 or 3 days and I have never regretted taking them.

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Just came across your most informative post today. Hope you're still doing well.

I too take probiotics (vivomixx 450 billion/LIFESTYLE labs) and am never sure of best time to take as there is conflicting advice on net. I have also been taking HCL without pepsin but will try your recommendation now. Took dig. enzs. a while back but cant say I noticed any benefit but difficult to assess when taking other stuff and making dietary/lifestyle changes.

Would love an update if you read this and have time.

Best wishes

Acid Drop


I would remove this statement I wrote :

Betaine hydrochloride with every meal and every snack.

I would now direct people to these links for better information on the appropriate use of Betaine HCL + Pepsin :



I ended up overdoing it and having to come off betaine because I had irritated my stomach. I intended to start taking it again but see below.

I also have doubts that digestive enzymes were helping and I no longer take them.

I still think probiotics should be taken at bedtime, with water and no food in the hope of getting some of the bacteria into my intestines alive. But I know there are some people who insist they must be taken with food. I don't understand the logic of that.

Things that I've found that help me :

Slippery elm at bedtime. I'm also considering trying marshmallow root which does a similar job to slippery elm.

L-Glutamine powder - one heaped teaspoon powder mixed with cold water after breakfast.


Psyllium seed husk powder - I take a small dose - one slightly heaped teaspoon which is only a quarter of the dose recommended by the manufacturer - mixed with the glutamine and cold water. I also mix it with a small amount of fruit squash to disguise the taste of the psyllium.

Kefir : I drink kefir because it is a good probiotic. I really need to start trying out more fermented foods and adding bone broth to my diet.

Magnesium citrate : Has a very mild laxative effect which I find helpful, and also helps prevent spasm in my gut.

Confession time : I no longer take betaine because I am taking NSAIDs (Naproxen) for pain. I can't live without the pain killers and I have to take ranitidine (Zantac) to cut my (already low) stomach acid. My doctor wanted me on PPIs but I refused them. Without ranitidine the naproxen feels like it is burning holes in my gut.

With my self-treatment of my various aches and pains I have managed to reduce the pain I have to some degree. If I could ever come off the NSAIDs I would definitely stop the ranitidine and take betaine again.


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