The thyroid is a gland that sits in the front of your neck and is part of the endocrine system.

It is responsible for creating and releasing hormones that regulate many vital body functions such as breathing, heart rate, body weight, menstrual cycles, body temperature, and central and peripheral nervous systems functions.

The most common two issues with the thyroid for persons with Lyme are Hashimoto’s thyroiditis and hypothyroidism.

Hashimoto’s is an autoimmune disease where the immune system attacks an otherwise healthy thyroid. Hypothyroidism is characterized by a deficiency in thyroid hormones which makes the thyroid under function.

Hashimoto’s thyroiditis

Lyme and co-infections, as well as mold and biotoxins, change the immune system so that it loses tolerance for things. Essentially, the immune system isn’t functioning properly and is attacking things it shouldn’t. Over a period of time, many people experience things like increased reactions to foods previously tolerated, increased reactions to environmental chemicals, odors, and pets.

Lyme causes an inflammatory reaction that affects the immune system (read more about this here). The immune system is no longer able to go after the pathogens that it should and cannot correct itself. It is confused and unable to figure out which is a pathogen it should attack and which is not. Molecular mimicry in Hashimoto’s thyroiditis suggests there is enough similarity in the appearance of infectious microbes (Lyme and co-infections) to that of thyroid tissues that the immune system attacks by mistake, causing tissue inflammation, and if this persists, tissue damage.

Over and above this issue, there are several other considerations regarding Hashimoto’s thyroid disease in people with a chronic disease like Lyme. These are amongst the most well-recognized factors leading to the onset or exacerbation in Hashimoto’s:

  • Environmental toxins
  • Stress for an extended period of time
  • Leaky gut
  • Parasites
  • Infections
  • Mold or biotoxin exposure
  • Physical trauma


Unlike Hashimoto’s, where the immune system gets confused and attacks the thyroid, many people with Lyme may have an under-functioning thyroid, or hypothyroidism, triggered by the Lyme and not the immune system.

The thyroid gland produces and regulates a couple of thyroid-specific hormones that are triggered by additional thyroid hormones produced in the hypothalamus and pituitary gland; Lyme can inhibit the function of the hypothalamus. This creates a domino effect, and the thyroid is one of the areas where problems appear.

This cascade, starting with Lyme causing the brain to malfunction, causes the thyroid to not convert thyroid hormones as it normally would.

Let’s talk about how you can support your thyroid health.

First, treating Lyme and co-infections is key.

Maintaining a healthy diet is also important (resources on a healthy diet can be found here).

Detox also helps remove some of the sources of trouble (tips can be found here).

Having leaky gut or inflammatory digestive issues is strongly linked not only to Hashimoto’s thyroid disease but also to numerous autoimmune and neurological degenerative diseases. Fixing your leaky gut will promote better immune tolerance, leading to improvement in Hashimoto’s and general thyroid health. Leaky gut and digestive issues can be a really big topic, so we are not going to try to tackle it here, but if you suspect you have digestive issues, you should work on identifying and correcting them for thyroid health.

Managing stress is important for thyroid health. Consider meditation and mindfulness as a way to decrease stress.