Burning sensation when I wake up

[Zuma888]

Hello everyone,

I am 30 years old, female, and have Hashimoto's thyroiditis and suspected celiac disease (wasn't able to complete a gluten challenge, but have the symptoms and HLA-DQ8) or at least some kind of gluten sensitivity.

When I first got diagnosed with Hashimoto's thyroiditis, I went on AIP and never reintroduced gluten. Whenever I would eat a little bit of gluten I would wake up feeling very old, achy, and unrested, with a burning sensation everywhere especially on my hip bones and chest area. It felt like severe inflammation. This would also happen during stressful times and times where I hadn't been sleeping well. 

This symptom had decreased in intensity and completely gone away before I tried to do a gluten challenge over a month ago. Now it is back and I have it every day when I wake up. It usually goes away or decreases in intensity after a few hours of being awake. Is this inflammation or something else, and is it related to Hashimoto's thyroiditis or celiac (or gluten sensitivity) or both? Could it be related to not moving for long periods of time (as is the case when I am sleeping)?

I was also extremely sensitive to all foods when I first started AIP about 3 or 4 years ago, but with time, I could tolerate more foods and even gluten in small amounts occasionally. Now my stomach is super sensitive, I am afraid to eat again, and my stools are abnormal.

Thank you.

[Zuma888]

I forgot to mention that exercise also triggers it, except for the period right before I tried the gluten challenge where I could do moderately intense workouts without getting this burning sensation and extreme fatigue for days afterwards.

[knitty kitty]

Hi, @Zuma888,

Hashimoto's commonly occurs with Celiac Disease.  Those HLA genes code for other autoimmune diseases along with Celiac.  Hashimoto's and Celiac overlap.  People with Hashimoto's produce anti gluten antibodies, so a gluten free diet is definitely a must.  It may be safe to assume you've got Celiac Disease as well.  

People with Hashimoto's often have deficiencies in Vitamin C and Thiamine.  Vitamin deficiencies are common in Celiac Disease.  A deficiency in Thiamine can manifest as Gastrointestinal Beriberi with digestive upsets and changes in bowel habits.  

Your burning sensation and extreme fatigue for days after working out may be due to a lack of Thiamine and B vitamins.  If you don't have sufficient Thiamine, lactic acid can build up in muscles causing that burning sensation.  Anybody remember Jane Fonda's workouts?  Her catch phrase was "Feel the burn" meaning work out so hard, lactic acid builds up causing the burning sensation.  Thiamine and the B vitamins are needed to clear that lactic acid and repair muscle damage.

Supplementing with a B Complex and Benfotiamine, a form of thiamine shown to promote intestinal healing, and magnesium would be beneficial to help you feel better.  Blood tests for vitamin deficiencies are inaccurate.  Take Thiamine and B vitamins, then look for health improvements.  If not needed or absorbed, excess B vitamins are easily excreted in urine.  

[Scott Adams]

The burning sensation you describe—particularly upon waking or after exercise—could indeed be related to systemic inflammation, which is common in autoimmune conditions like Hashimoto's and celiac disease. Gluten exposure, even in small amounts, may trigger an immune response that exacerbates inflammation, leading to the achiness and burning you feel, especially in areas like your hips and chest. Stress and poor sleep can further worsen inflammation, creating a cyclical effect. The fact that these symptoms improved before your gluten challenge but returned afterward strongly suggests a connection to gluten sensitivity. Additionally, prolonged immobility during sleep might contribute to stiffness or discomfort, but the burning sensation points more toward an inflammatory or neurological component. Your heightened food sensitivities and digestive issues could indicate ongoing gut dysfunction, possibly due to intestinal permeability ("leaky gut") from gluten exposure or autoimmune activity. Since exercise also triggers symptoms (except during your remission period), it may be worth exploring gentle movement like yoga or walking to avoid overexertion while supporting circulation. Consulting a healthcare provider familiar with autoimmune conditions—particularly one who can guide you through targeted testing for celiac (without a full gluten challenge) or assess for other triggers like histamine intolerance—might help clarify next steps. In the meantime, prioritizing anti-inflammatory foods, stress management, and restorative sleep could provide some relief.

[Zuma888]

21 hours ago, knitty kitty said:

Hi, @Zuma888,

Hashimoto's commonly occurs with Celiac Disease.  Those HLA genes code for other autoimmune diseases along with Celiac.  Hashimoto's and Celiac overlap.  People with Hashimoto's produce anti gluten antibodies, so a gluten free diet is definitely a must.  It may be safe to assume you've got Celiac Disease as well.  

People with Hashimoto's often have deficiencies in Vitamin C and Thiamine.  Vitamin deficiencies are common in Celiac Disease.  A deficiency in Thiamine can manifest as Gastrointestinal Beriberi with digestive upsets and changes in bowel habits.  

Your burning sensation and extreme fatigue for days after working out may be due to a lack of Thiamine and B vitamins.  If you don't have sufficient Thiamine, lactic acid can build up in muscles causing that burning sensation.  Anybody remember Jane Fonda's workouts?  Her catch phrase was "Feel the burn" meaning work out so hard, lactic acid builds up causing the burning sensation.  Thiamine and the B vitamins are needed to clear that lactic acid and repair muscle damage.

Supplementing with a B Complex and Benfotiamine, a form of thiamine shown to promote intestinal healing, and magnesium would be beneficial to help you feel better.  Blood tests for vitamin deficiencies are inaccurate.  Take Thiamine and B vitamins, then look for health improvements.  If not needed or absorbed, excess B vitamins are easily excreted in urine.  

Thanks! I am currently trying B1 out on its own. I tried many brands of B-complex and they always make me feel nauseous and tired. I think I may have to try taking each B vitamin on its own.

[Zuma888]

19 hours ago, Scott Adams said:

The burning sensation you describe—particularly upon waking or after exercise—could indeed be related to systemic inflammation, which is common in autoimmune conditions like Hashimoto's and celiac disease. Gluten exposure, even in small amounts, may trigger an immune response that exacerbates inflammation, leading to the achiness and burning you feel, especially in areas like your hips and chest. Stress and poor sleep can further worsen inflammation, creating a cyclical effect. The fact that these symptoms improved before your gluten challenge but returned afterward strongly suggests a connection to gluten sensitivity. Additionally, prolonged immobility during sleep might contribute to stiffness or discomfort, but the burning sensation points more toward an inflammatory or neurological component. Your heightened food sensitivities and digestive issues could indicate ongoing gut dysfunction, possibly due to intestinal permeability ("leaky gut") from gluten exposure or autoimmune activity. Since exercise also triggers symptoms (except during your remission period), it may be worth exploring gentle movement like yoga or walking to avoid overexertion while supporting circulation. Consulting a healthcare provider familiar with autoimmune conditions—particularly one who can guide you through targeted testing for celiac (without a full gluten challenge) or assess for other triggers like histamine intolerance—might help clarify next steps. In the meantime, prioritizing anti-inflammatory foods, stress management, and restorative sleep could provide some relief.

Thanks! This makes a lot of sense.

[knitty kitty]

2 hours ago, Zuma888 said:

Thanks! I am currently trying B1 out on its own. I tried many brands of B-complex and they always make me feel nauseous and tired. I think I may have to try taking each B vitamin on its own.

Please be sure to try Benfotiamine or Thiamine Hydrochloride.  The form Thiamine Mononitrate is not absorbed nor utilized well.  Benfotiamine is much more bioavailable.  Perhaps Thiamine Mononitrate was in your previous B Complex supplements, explaining why they didn't work for you.  

All the B vitamins work together.  Thiamine needs the other B vitamins to make enzymes and ATP, so you will need to take them.  Taking them in individual supplements is fine.  I've done the same.  Just remember you need all eight.  

Let me know how it's going for you!

[Healthforme]

Does one need to get a prescription for Thiamine Hydrochloride? 

[trents]

No. It's over the counter. Readily available on Amazon. Good bio availability but shelf-life is not as good as thiamine mononitrate which is the most common form found in over the counter vitamin products.

Edited August 10, 2025 by trents

[Zuma888]

On 8/5/2025 at 7:37 PM, knitty kitty said:

Please be sure to try Benfotiamine or Thiamine Hydrochloride.  The form Thiamine Mononitrate is not absorbed nor utilized well.  Benfotiamine is much more bioavailable.  Perhaps Thiamine Mononitrate was in your previous B Complex supplements, explaining why they didn't work for you.  

All the B vitamins work together.  Thiamine needs the other B vitamins to make enzymes and ATP, so you will need to take them.  Taking them in individual supplements is fine.  I've done the same.  Just remember you need all eight.  

Let me know how it's going for you!

I am taking thiamine hydrochloride. It's been over a week, and the burning seems to be gone. I am also taking a lower dose B complex with iron. Thank you so much for your help!

[knitty kitty]

@Zuma888, 

I'm so happy you're feeling better!  

Thanks for letting us know of your improvement!

[knitty kitty]

@Healthforme,

No prescription needed for thiamine hydrochloride, Benfotiamine, and TTFD (Tetrahydrofurfuryl Disulfide).  They are available over the counter.  

Thiamine Mononitrate is not recommended because the body doesn't absorb or utilize it well.