Supplements for Hashimoto's disease

In addition to a smartly-designed dietary protocol, supplements can help you in your Hashimoto’s healing journey, especially if your digestion is impaired, which prevents you from extracting enough nutrients from food.

You may be able to discontinue most supplements once your digestion is fixed and you have adopted a well-balanced diet suited for your own individual biochemistry.

“Start Low and Go Slow”

Supplements should be started at a low dose, one at a time.

Vitamins and herbs are certainly not without risks, even if they are ‘naturally-derived’. (Remember, arsenic is also a natural substance!)

You want to make sure to start at a low dose of one supplement one at a time, rather than starting the full dose of six different supplements at once.

For example, you may add selenium at 200 mcg and see how you tolerate it for a few days before you decide to increase it to 400 mcg.

Once you’ve found that you tolerate the 400 mcg dose for a few days, you can add a second supplement.

This approach increases the likelihood of catching adverse events before they get too far, and it will help you pinpoint the substance causing the adverse effect without having to stop all of your other supplements and delay your progress.

Not All Supplements Are Created Equally

Vitamin and supplement companies are not required to adhere to the same strict rules as medications in their manufacturing and labeling requirements.

This leads to some supplements not having the ingredients stated on their labels or having them in doses that are either too high or too low.

In some cases, they may contain substances not even listed on the label.

Additionally, many of the excipients used in drug store brands can cause hypersensitivity reactions as well as preventing the proper absorption of the supplement.

Reports of toxicity from poorly regulated supplements pop up every so often, and many brands are simply not worth spending your money on or risking your health over.

Formulations Matter

Various formulations exist for mineral supplements. For example, zinc is available as zinc oxide, zinc citrate, zinc gluconate, and zinc picolinate.

The picolinate formulation is the most bioavailable for zinc and chromium supplements.

Taking zinc with food or with vitamin C increases its absorption.

The same is true for iron supplements, which should be taken after a meal with vitamin C.


When beginning using supplements, the ideal approach is to always “start low and slow”.

This is especially true with probiotics as they can cause significant die-off symptoms.

This can cause further inflammation and autoimmune damage from endotoxins being released from the dying pathogenic flora as they are displaced by the beneficial bacteria in probiotics.

Since people with Hashimoto’s usually have low levels of alkaline phosphatase to begin with, they are unable to keep up with the daily endotoxin release from the normal life cycle of pathogenic bacteria, let alone the massive amounts released when bacteria start dying off at a fast rate.

That said, most probiotics in health food stores have maintenance doses of beneficial bacteria- doses that are too low to heal and make an impact on intestinal flora.

A super-extensive, high-potency probiotic supplement may contain 10 billion CFUs per capsule, while the minimal therapeutic dose for changing the gut flora is 60 billion CFUs.

For adults, we advise starting with a 10 billion CFU dose and increasing every few days until die-off is seen.

For a properly-functioning immune system, we need a balance of approximately 85 percent beneficial to 15 percent of potentially pathogenic bacteria.

The human intestines have been found to host between 7 and 50 percent of gram-negative bacteria.

It is unclear how many CFUs of beneficial bacteria it takes to displace one CFU of pathogenic bacteria.

Providing one trillion CFUs of beneficial bacteria seems like a lot, however, it may pale in comparison with the 16-50 trillion pathogenic bacteria that may be present in gut dysbiosis.

Probiotic supplements do not seem to take up residence in our intestines permanently and are described as transitional, meaning they do not grow in the intestines.

Beneficial bacterial species found on raw lacto-fermented vegetables reportedly contain trillions of CFUs per dose.

Although not technically supplements, they really are the superstars for overcoming dysbiosis and should be included in the healing plan above all else.

How to Get the Most Benefits From Your Supplements

As healthcare professionals, we know that adherence to a medication / supplement regimen can oftentimes be difficult.

Adherence studies have found that even when we know how to treat a condition perfectly well, in many cases when a product is recommended by a health care professional, it does not help the patient for a variety of reasons- most of them having to do with the lack of information the patient received.

  1. The patient never gets the product.
  2. The patient gets the wrong product, wrong dose, or wrong type of medication or supplement. 
  3. The patient gets the correct product but uses it incorrectly.
  4. The patient gets the product and knows how to use it but forgets to take it and uses the product only sporadically.

There is an old doctor’s joke about a man who goes to the doctor and says the suppositories the doctor prescribed are not working for his constipation.

Puzzled, the doctor asks, “How have you been using them?”

The patient replies, “Well, I swallow them, of course- what else would you do with them?”

You can spend hundreds of dollars on really great products, but if you don’t use them correctly (or at all), you might as well be throwing your money away!

Some medications and supplements cannot be absorbed in combination with other supplements or when food is present.

Others absorb better with food or other supplements.

Still others may need to be taken at different times of the day due to their propensity to cause tiredness or alertness.

Thyroid hormones in particular have a lot of restrictions.

They need to be taken on an empty stomach, thirty minutes prior to meals, and at least four hours apart from iron, calcium, and magnesium (which can lower the absorption of the hormone).

During the transition period, you may take multiple supplements.

Sometimes, it’s challenging to keep them all straight. We highly recommend purchasing a pill planner.

Stackable pill planners can be very useful as they can be thrown in your purse or pocket when you need to take supplements to work or on the road.

Attaching the supplements to a habit you already have (like brushing your teeth or making tea) may help, too.

Pill reminders can be sent to your smartphone using free apps courtesy of pharmaceutical companies (i.e. MyMedSchedule Plus). 

Sample Supplement Protocol

Morning Supplements (best on an empty stomach)

Bathroom (next to your toothbrush; take right before you brush your teeth)

  • Thyroid Hormone (ideally wait 60 minutes before eating for maximum absorption)
  • Selenium 200-400 mcg
  • Adrenal Glandular
  • Vitamin E 400 IU
  • Licorice drops (do not take if you have high blood pressure)
  • Thyroid Glandular (may be used as a natural substitute for thyroid medication. Take only if you are not on medication yet or tapering off)
  • Adrenal Adaptogens

Fridge (next to your breakfast foods)

Breakfast (next to your tea kettle)

Lunchtime Supplements (best with meals)

Put supplements in your lunch bag.

Note: Take NAC after you eat, as it will cause a stomachache without food.

Dinnertime (best with meals)

  • Betaine with pepsin. If you are vegan you can use a product without pepsin, such as HCL Breakthrough

If you forgot to take your lunch supplements, you can take them at dinner, but note that B vitamins can be stimulatory.

Bedtime (may be sedating)

Supplement Guide

Note: These statements have not been evaluated by the Food and Drug Administration (FDA). The products discussed are not intended to diagnose, treat, cure, or prevent any disease.

NameRationaleSide EffectsNotes
Adrenal Adaptogens Help support adrenal functionMultiple formulations exist; cross-check ingredients for sensitivites
B12Proper development of villi, protein digestion, many other benefitsBright yellow urineSublingual B12 may be better absorbed, especially with GI issues
Betaine with PepsinHelps digest proteinsBurning in throat; not to be used with ulcers!Take with meals containing protein
ChromiumRequired nutrient for thyroid functionMay cause drowsiness
CurcuminReduces inflammationCan alter liver enzymes, thin the blood, and change kidney functionLook for absorbable formulations with piperine, such as Curcumin Plus
Vitamin D 5,000 IUReduces inflammation, autoimmune symptomsIdeally, you should get it from the sun, but supplements can be a secondary option; can measure levels
Vitamin E 400 IUAntioxidant, works synergistically with selenium, improves skinCan have blood-thinning effects
GlutamineHelps repair the intestinal liningAgitationDiscontinue if experiencing agitation
N-Acetyl-CysteineHelps restore the gut lining; powerful antioxidant; supports liver function; helps eliminate pathogenic bacteriaStomach pain if taken on empty stomachTake with food!
LicoriceAntiviral properties; helps stretch cortisol levels in cases of adrenal fatigue / exhaustionMay increase blood pressure; avoid if already have high blood pressure
MagnesiumHelps restore DHEA levelsDiarrhea, sleepinessDepleted by fluoride; most people show deficiency
Omega-3 or Cod Liver OilReduces inflammation; improves skin conditionCan have blood-thinning effectsLook for formulations free of mercury
Probiotics or VSL#3Lactobacillus deficiency; LB creates enzymes that aid digestion and absorption, help impove immune function, and help balance out pathogenic floraNausea, vomiting, die-off reactionProbiotic levels can be measured by stool tests (CDSA, GI Effects)
Proteolytic enzymesReduce circulating immune complexes of proteins that may become antigenicTake between meals
Saccharomyces boulardiiIncreases SIgA; helps clear out pathogenic bacteria from the bodyCombine with other probiotics; dosages higher than stated on the package may need to be taken
Selenium 200 mcgAntioxidant; reduces TPO antibodies; helps convert T4 to T3.

Will not be absorbed properly from multivitamin or Brazil nuts
Toxicity reported at excessive doses, garlic smell sign of excessive doseMake sure to rule out iodine deficiency; can make hypothyroidism worse if selenium is given in overt iodine deficiency

Take on an empty stomach along with vitamin E
Thyroid Glandular (protomorphogen)Reduces antibodies; helps rebuild thyroid.

Natural and effective alternative to thyroid medication if it’s not well tolerated
Hyperthyroid symptoms Start with 1 capsule and increase gradually; recheck antibodies after starting
ZincRequired for T4 to T3 conversion.

Deficiency due to impaired absorption with Hashimoto’s, Celiac; seen as low alkaline phosphatase on CBC
May cause copper deficiency in doses >30 mg/dayLiquid deficiency test: swish around mouth

Picolinate version is absorbed best. Take with liposomal vitamin C and food.

PS. If you haven’t already, you may check out our Recommendations List for high-quality supplements, health products and services you can trust. There is probably nothing health-related you won’t find there + special discounts are waiting for you.

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About George Kelly


This content is for informational and educational purposes only. It is not intended to provide medical advice or to take the place of such advice or treatment from a personal physician. All readers/viewers of this content are advised to consult their doctors or qualified health professionals regarding specific health questions. Neither Metabolic Body nor the publisher of this content takes responsibility for possible health consequences of any person or persons reading or following the information in this educational content. All viewers of this content, especially those taking prescription or over-the-counter medications, should consult their physicians before beginning any nutrition, supplement or lifestyle program.