If you suspect you’re experiencing symptoms of Hashimoto’s flare ups, there are two very different possible causes:
Immune system activation and inflammation (often linked to a gut health or female hormone imbalance)
Low thyroid function (hypothyroid)
Standard healthcare for Hashimoto’s disease tends to focus on treating hypothyroidism. But this is only part of the equation, and it leaves many patients struggling with unresolved symptoms. In fact, contrary to what many believe, the majority of Hashimoto’s patients don’t actually develop hypothyroidism at all .
Hashimoto’s disease itself is an autoimmune disease in which the immune system attacks the thyroid gland, and it’s marked by elevated thyroid antibodies. But these changes occur gradually, meaning that it’s unlikely for a flare of symptoms to be caused by a surge in antibodies associated with Hashimoto’s. There’s likely something else at play– often a gut or female hormone imbalance, which we’ll cover in more detail below. In this article, we’ll explore how you can calm your immune system, lower inflammation, and feel better. But first, let’s take a closer look at the two distinct reasons for Hashimoto’s symptoms.
Symptoms of Hashimoto’s Flare Ups May Not Be What You Think
If you’ve been diagnosed with Hashimoto’s and you’re experiencing a sudden burst of symptoms, it’s natural to assume that it’s the Hashimoto’s itself that’s flaring up and causing the problem. But in fact, it’s unlikely for a Hashimoto’s “flare up” to be the cause of your symptoms. That’s because Hashimoto’s generally causes slow, subtle changes to the thyroid gland over the course of many years, which suggests that the TPO antibodies that characterize Hashimoto’s are not likely to be causing symptoms.
Studies of correlations between TPO antibodies and symptoms have suggested that high TPO antibodies are not associated with reduced quality of life or disease severity in general [2, 3]. Instead, symptoms that occur for those with Hashimoto’s are more likely to be caused by underlying gut imbalances or female hormone imbalances, rather than by Hashimoto’s or the elevated antibodies it’s associated with.
Immune System Activation
Hashimoto’s disease is an autoimmune disorder that affects thyroid function. As with all autoimmune diseases, the body’s immune system attacks its own tissues in a case of mistaken identity. With Hashimoto’s, this overzealous immune response causes thyroid inflammation or thyroiditis.
When you experience symptoms of Hashimoto’s flare-up, you’re likely having an autoimmune flare. This means that your immune system has gone into overdrive and is generating inflammation.
For many thyroid patients, the root cause of an inflammatory flare is linked to poor gut health in what’s known as the gut-thyroid connection . Improving your gut health can calm inflammation, reduce symptoms of a Hashimoto’s flare up, and decrease thyroid autoimmunity [5, 6, 7, 8, 9, 10, 11, 12]. It may also be related to an imbalance of the female hormone estrogen (which can often be rooted in gut issues too).
Low Thyroid Function
Over time, the inflammatory process can damage the thyroid gland and impair thyroid function, eventually leading to thyroid issues like hypothyroidism.
It’s important to note that although Hashimoto’s is the most common cause of hypothyroidism, not everyone who has Hashimoto’s has hypothyroidism. In fact, in the majority of cases, Hashimoto’s does not lead to hypothyroidism– only 9-19% of individuals with the autoimmune condition develop hypothyroidism .
The idea that Hashimoto’s automatically means hypothyroidism is a common misconception that can lead to overtreatment of thyroid issues when thyroid hormone levels are actually not a problem.
If you do have hypothyroidism, your thyroid gland does not produce enough T4 thyroid hormone (thyroxine). Your bloodwork may also show high TSH (thyroid stimulating hormone), which is produced by the pituitary gland and used to make T4. When you have impaired thyroid function, TSH is underutilized, so the number gets higher. The disruption of low T4 causes your metabolism to slow down. Symptoms of hypothyroidism (underactive thyroid), include:
Decreased heart rate
Inconsistent menstrual cycle
Hypothyroidism is easily treated with thyroid replacement hormone. Levothyroxine (Synthroid) is the most commonly prescribed thyroid medication.
If you are taking thyroid medication and your lab results are normal, you shouldn’t experience symptoms of hypothyroidism. However, many patients do continue to struggle with tiredness, brain fog, poor mood, and other symptoms, despite taking medication.
In this case, your symptoms are likely caused by inflammation and dysfunction in the gut-thyroid connection, not a lack of thyroid hormone.
The Gut-Thyroid Connection
Fatigue, brain fog, and mood issues aren’t just associated with autoimmune thyroid disease. They are also common symptoms of gut disorders. And while Hashimoto’s and hypothyroidism affect 1-2% and 0.6% of the population respectively, functional gastrointestinal disorders affect an estimated 40% [13, 14].
Here are a few examples:
More than 50% of IBS (irritable bowel syndrome) patients have symptoms of fatigue, according to a meta-analysis of 17 studies .
Sixty-eight percent of patients with suspected non-celiac gluten sensitivity reported a lack of well-being . These patients also reported tiredness (64%), headache (54%), anxiety (39%), brain fog (38%), and other non-digestive symptoms.
In a systematic review, IBS patients were three times as likely as healthy subjects to have either anxiety or depression .
Depression is prevalent in both IBS and IBD (inflammatory bowel disease) patients .
Other studies associate gut conditions with sleep disorders , headaches [16, 20], dermatitis , rosacea , and joint pain .
Gut health and thyroid health go hand-in-hand, as do gut health and many other systems in your body. While there may be a genetic component to predispose a person to thyroid issues or other autoimmunity, there’s a good chance that poor gut health can turn those genes on. Likewise, improving gut health can help quell, lessen, or even eliminate the problem.
Female Sex Hormones and Thyroid
When your endocrine system (the system in your body that regulates all sorts of hormones, including thyroid hormone, stress hormones, and sex hormones) goes haywire, you can experience a lot of the same symptoms as when you have poor gut health. This includes mood swings, irritability, headache, fatigue, constipation, abdominal cramping, anxiety, insomnia, and more .
Hormones are powerful chemicals. Understanding the feedback loop between gut health and hormonal health — especially how stress plays a role in disrupting balance — in addition to the interplay within the greater endocrine system (sex hormones, thyroid hormones, and others that may be affected) might help you get to the root cause of your flare ups a lot more successfully.
Stress is a major factor across the spectrum of challenges I’ve just enumerated. When you experience stress, your body puts energy toward creating stress hormones like cortisol rather than creating sex hormones like estrogen and testosterone. It also puts more energy into fight or flight, sending blood to your muscles rather than putting energy toward digesting your food.
High levels of stress also increases gut permeability (leaky gut) and negatively impacts your gut microbiome [25, 26]. Interestingly, female hormonal fluctuation can also affect your digestion (you may experience digestive upset as a PMS symptom, for example) .
What Happens to Thyroid Health When Gut Conditions Are Treated?
Treating the gut has been shown to have a direct, positive impact on thyroid health. For example:
One small study found a remarkable drop in TPO antibodies (a marker of autoimmune thyroiditis) when patients were treated for H. pylori gut infections . Other studies show that treating H. pylori can improve TSH levels [6, 7, 11].
Treating Blastocystis hominis (a parasitic gut infection) has been shown to reduce inflammatory markers, thyroid antibodies, and TSH levels .
Gut treatments have also been shown to improve thyroid-like symptoms, including fatigue [28, 29, 30], mild to moderate depression , and anxiety .
Eliminating common trigger foods can also be helpful for some thyroid patients. In one study, lactose restriction led to a significant decrease in TSH levels for thyroid patients with lactose intolerance . Another study found that a gluten-free diet reduced the need for thyroid medication in patients with atypical celiac disease .
Improving your gut health is an important part of an overall plan for better thyroid health.
How to Prevent Symptoms of Hashimoto’s Flare-Ups
If you have Hashimoto’s disease and struggle with symptoms of “Hashimoto’s flare-ups”, there’s a lot you can do to feel better and regain your energy.
Take a step-by-step approach to address the most fundamental health and wellness foundations first. For some patients, symptoms will start to resolve after taking a few steps. Other patients will need to complete more steps.
1. Get Your Thyroid Hormone Levels in Range
An important first step is to resolve true hypothyroid symptoms with medication. Keep in mind that while thyroid hormone medication is important for those with true hypothyroidism, it has been found not to be helpful for those with subclinical hypothyroidism (in spite of it commonly and erroneously being prescribed for the latter) [33, 34]. If you’re unsure, you can use the guide here to help you and your practitioner interpret your thyroid test results.
If you identify any of these issues as problem areas for you, take steps to improve your lifestyle and work on practicing better self-care.
3. Eat an Anti-Inflammatory Diet
Eating a simple, real food diet is the foundation of gut and thyroid health. A healthy diet can reduce the burden of inflammation in your body, improve your gut health, and reduce symptoms [35, 36, 37, 38, 39].
There’s no one-size-fits-all thyroid diet. However, these dietary approaches are often helpful:
Don’t eat processed foods. Eat foods free of additives and chemical preservatives.
You can try a lower-carb diet. It was shown in one study to reduce thyroid antibodies by 44% in people with Hashimoto’s thyroiditis (but not celiac disease) .
Identify and remove foods that trigger your symptoms. A gluten-free diet(or gluten-reduced) may help reduce antibodies .
A low-iodine diet or avoiding supplemental iodine sources may be helpful for thyroid patients .
If you want to follow a specific diet template or meal plan, the paleo diet is anti-inflammatory, lower in carbs and trigger foods, and suitable as a long-term diet.
If a paleo-type diet doesn’t resolve all of your symptoms, the AIP diet (autoimmune paleo or autoimmune protocol) is a good next step. The AIP diet is an elimination diet intended to help you identify food triggers that cause inflammatory symptoms. In extreme or severe cases, you might consider a gut reset with the elemental diet. It’s been shown to help with gas, bloating, and other digestive issues. However, seek medical advice regarding this diet.
4. Take Probiotics
Probiotics are effective because they work to balance the community of microorganisms that live in your gut , fight harmful microorganisms [44, 45, 46], promote a healthy immune response [47, 48, 49], and reduce inflammation .
A study of hypothyroid patients found that probiotic supplements reduced the need for thyroid medication and reduced fatigue .
5. Take Supplements
Vitamin D may improve your thyroid health and lower thyroid antibodies [50, 51, 52]. Safe sun exposure is free and the most bioavailable way to get adequate vitamin D. Supplemental vitamin D is recommended during winter months in higher latitudes.
Selenium supplements can reduce TPO antibodies in thyroid patients [53, 54]. However, long-term supplementation is less beneficial [55, 56]. Consider 3-6 months of supplementation to boost your selenium levels.
Supplementing with HCI (betaine hydrochloride) can increase stomach acid levels, and may help with the absorption of iron, vitamin B12, and thyroid medication. Up to 40% of hypothyroid patients may have low stomach acid [57, 58].
Some thyroid patients may benefit from iron supplementation. If your blood tests show serum ferritin (the storage form of iron) levels significantly below 100 mg/l with iron, supplementing with iron may help to improve fatigue .
6. Treat Gut Infections
If lifestyle improvements, diet, and probiotics haven’t fully resolved your symptoms, the next step is to look for hidden gut infections.
Research shows a correlation between thyroid problems and gut infections, including SIBO (small intestinal bacterial overgrowth) [60, 61], H. pyloriinfection [62, 63], and B. hominis infection .
Testing for and treating gut infections is best done with the help of an experienced health practitioner.
7. Adjust Thyroid Medications
As your gut health improves, you may absorb your thyroid medication better. Lab tests and consultation with your doctor can help to determine if you need to fine tune your thyroid medication. This is important, as you don’t want to go too far in the wrong direction and send yourself into hyperthyroid, which has a whole other list of symptoms (including heart palpitations).
Thyroid tests for TPO antibodies measure the degree of autoimmune activity in Hashimoto’s disease . TPO levels over 35 IU/mL are generally considered positive for autoimmunity.
Many patients are able to significantly reduce TPO levels through diet and lifestyle changes or by treating a gut infection. However, you don’t need to lower your TPO levels to zero. In fact, striving to do so can create stress and be counterproductive.
Research shows that patients with TPO levels below 300 are unlikely to become hypothyroid  and patients with TPO levels below 500 have minimal risk of becoming hypothyroid . Essentially, there is not enough autoimmune activity to significantly damage the thyroid gland at these levels.
If your TPO levels are high, a sensible goal is to get your TPO level below 500.
You Don’t Need to Be Tired and Frustrated with Hashimoto’s
If you struggle with ongoing symptoms, keep in mind that more thyroid medication may not be the answer. Even if your symptoms are not necessarily symptoms of Hashimoto’s flare ups, they can usually be improved by addressing underlying imbalances that are contributing to inflammation.
Poor gut health is a very common cause of symptoms like fatigue, brain fog, poor mood, weight gain, and more. This may be a bigger contributor to your symptoms than your thyroid hormone levels or thyroid antibody levels.
Luckily, focusing on your gut health and attending to your daily habits like sleep or stress management can help you manage and resolve symptoms. For more individualized guidance, reach out to our functional health center.
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