Does Hashimoto’s Cause Stomach Pain? Making the Connection Between the Thyroid and Your Gut

Are you dealing with persistent stomach pain, bloating, acid reflux, or digestive discomfort that never seems to fully go away? 

Maybe you’ve tried changing your diet, taking over-the-counter remedies, or avoiding certain foods, but nothing has provided lasting relief. When digestive symptoms become chronic, they may be a sign that something deeper is affecting your health.

For many people, there’s a surprising connection between gut health and autoimmune conditions like Hashimoto’s disease. Hashimoto’s can affect much more than the thyroid; it can also cause problems with digestion, inflammation, and nutrient absorption.



In this article, you’ll learn how Hashimoto’s may contribute to stomach pain and digestive symptoms, along with holistic strategies that may help support both thyroid and gut health.

Table of Contents

Hashimoto’s disease is an autoimmune condition that affects the thyroid gland and commonly leads to hypothyroidism, or low thyroid hormone levels. While stomach pain is not typically considered a primary symptom of Hashimoto’s itself, many people with the condition experience digestive issues that may contribute to abdominal discomfort.



Because thyroid hormones help regulate metabolism and digestion, low thyroid function can slow movement throughout the digestive tract. This may increase the likelihood of symptoms such as bloating, constipation, acid reflux, indigestion, and stomach pain.

Additionally, people with Hashimoto’s may be more likely to experience related gastrointestinal conditions, including:

• IBS
• Gastritis
• Food sensitivities
• Other autoimmune disorders that can affect gut health

Hashimoto’s disease can affect much more than the thyroid gland. Because thyroid hormones play an important role in regulating digestion, changes in thyroid function may impact how the gastrointestinal tract processes and moves food.



One of the most common effects of hypothyroidism is slowed gut motility, meaning food moves more slowly through the digestive tract. This may contribute to symptoms such as constipation, bloating, gas, indigestion, and abdominal discomfort.

Hashimoto’s may also influence digestion in other ways, including:

• Reduced stomach acid production: Low thyroid hormone levels may decrease stomach acid, which can make it harder to properly break down food and absorb nutrients.
• Changes in digestive enzymes: Impaired digestion may contribute to feelings of fullness, bloating, or stomach pain after meals.
• Autoimmune-related inflammation: Chronic inflammation associated with autoimmune disease may affect the stomach lining and intestinal tract in some individuals.
• Gut microbiome imbalances: Some research suggests that imbalances in gut bacteria may play a role in digestive symptoms and immune system function in people with autoimmune conditions.

Because the gut and immune system are closely connected, digestive symptoms may sometimes become more noticeable when Hashimoto’s is poorly managed or accompanied by other gastrointestinal conditions.

Hashimoto’s patients may experience stomach pain for a variety of reasons. We’ll discuss some of the most common ones below.



If you’re bothered by Hashimoto’s and stomach pain, contact HealthierU for a free consultation. Dr. Donna Sergi offers a holistic approach to proper nutrition and natural remedies that can help treat your symptoms and your condition.

Digestive symptoms are common in people with Hashimoto’s disease and may range from mild discomfort to chronic gastrointestinal problems.



Because thyroid hormones help regulate digestion, low thyroid function associated with Hashimoto’s may slow the digestive process and contribute to symptoms like indigestion,

When sphincter muscles don't work well, food might stay in one part of the digestive tract too long.



Patients with Hashimoto's disease often have weak lower esophageal sphincters, which means it doesn't close tightly enough to prevent stomach acid from entering the esophagus.

A range of symptoms may accompany indigestion, such as: 

• Heartburn
• Nausea
• Belching
• Acidic taste
• Regurgitation

The severity and duration of these symptoms might vary from person to person.

Constipation is another common digestive complaint among people with Hashimoto’s disease. Thyroid hormones help regulate muscle contractions throughout the digestive tract, including the colon. When thyroid hormone levels are low, digestion may slow down, causing stool to move more slowly through the intestines.



As waste remains in the colon longer, more water is absorbed, which can lead to harder, more difficult-to-pass stools. One major symptom of constipation is abdominal discomfort or pressure.

Thyroid hormones also influence stomach acid production, digestive enzymes, and intestinal motility. When digestion slows, food may remain in the GI tract longer than normal, increasing the likelihood of gas buildup and bloating.

Incomplete digestion can also contribute to fermentation in the gut, which may lead to abdominal pressure and discomfort.

Common, often painful, symptoms of bloating include:



• Abdominal swelling or distension
• A feeling of fullness or tightness
• Increased gas
• Cramping or abdominal discomfort
  

Gastritis is inflammation of the stomach lining, which may cause: 

• Stomach pain
• Indigestion
• Discomfort

Although Hashimoto’s does not directly cause gastritis, people with autoimmune conditions may have a higher risk of developing autoimmune gastritis. Both conditions involve an immune system response that mistakenly attacks healthy tissues.

In some cases, chronic inflammation associated with autoimmune disease may also affect stomach acid production and digestion. Reduced stomach acid levels can interfere with the absorption of important nutrients, including vitamin B12, which may contribute to additional health concerns over time.

Celiac disease is an autoimmune condition in which the immune system reacts to gluten, a protein found in wheat, barley, and rye. This immune response damages the lining of the small intestine and may interfere with nutrient absorption.

Research suggests that people with Hashimoto’s thyroiditis may have a higher risk of developing celiac disease because both conditions are linked to immune system dysfunction and shared genetic factors associated with autoimmunity.

Common symptoms of celiac disease may include abdominal pain, cramping, and bloating/gas, among others.



Because symptoms can overlap with Hashimoto’s-related digestive issues, individuals with Hashimoto’s who experience persistent gastrointestinal symptoms may benefit from discussing celiac disease screening with their healthcare provider.

Irritable bowel syndrome (IBS) is a common gastrointestinal condition that affects how the digestive tract functions. While IBS is not directly caused by Hashimoto’s disease, some people with Hashimoto’s may also experience IBS symptoms, potentially due to changes in gut motility, inflammation, stress, or overlapping immune system dysfunction.

Among other symptoms, IBS may cause chronic stomach pain or cramping, bloating, and excess gas.



In some cases, thyroid hormone imbalances associated with Hashimoto’s may slow digestion and contribute to gastrointestinal discomfort that resembles or worsens IBS symptoms. Food sensitivities and changes in the gut microbiome may also play a role.

Small intestinal bacterial overgrowth (SIBO) occurs when excessive bacteria grow in the small intestine, potentially leading to digestive symptoms and nutrient absorption problems. People with Hashimoto’s may have a higher risk of developing SIBO because slowed gut motility can allow bacteria to accumulate in the digestive tract.



Treatment for SIBO often involves addressing bacterial overgrowth while also supporting healthy digestion and thyroid function. For people living with Hashimoto’s, managing thyroid hormone levels may help improve gut motility and digestive symptoms over time.

In some cases, medications used to manage hypothyroidism associated with Hashimoto’s disease may contribute to digestive discomfort or mild gastrointestinal side effects. Although stomach pain is not a common side effect, some people may experience nausea, cramping, bloating, or stomach irritation when starting or adjusting medication.

Taking thyroid hormone replacement medication exactly as prescribed may help reduce the likelihood of digestive side effects. These medications are often recommended on an empty stomach, typically in the morning, to support proper absorption.

If stomach pain or digestive symptoms persist after starting thyroid medication, it is important to speak with a healthcare provider. In some situations, dosage adjustments, timing changes, or alternative formulations may help improve tolerance.



For most individuals, the benefits of properly managing Hashimoto’s outweigh the risk of mild digestive side effects, especially because untreated thyroid hormone imbalances can also contribute to gastrointestinal symptoms.

Autoimmune Protocol (AIP) is an elimination diet designed to help people with autoimmunity determine food allergies and sensitivities, reverse nutrient deficiencies, and balance gut flora.



AIP involves removing foods most likely to cause problems for people with autoimmune diseases, such as: 

• Grains
• Beans
• Legumes
• Dairy
• Eggs
• Nuts
• Seeds
• Food additives

A wide variety of fruits and vegetables are included in the diet, as well as nutrient-dense foods like bone broth, high-quality meat, and wild-caught fish.

During the elimination phase, which may last anywhere from several weeks to several months, you monitor how your body responds as certain foods are removed from your diet. As foods are gradually reintroduced one at a time, you may be able to identify ingredients that trigger symptoms or interfere with your progress. 

This process can help you develop a more personalized eating plan that supports your overall healing and long-term health goals.

Irritable bowel syndrome and other gastrointestinal disorders may be managed with the low FODMAP diet. 

People with sensitive guts may experience intestinal issues due to carbohydrates and sugar alcohols, which are poorly absorbed in the small intestine. The low FODMAP diet restricts foods high in fermentable carbohydrates to identify specific triggers, then gradually reintroduces them. 

The most common high-FODMAP foods include: 

• Fruits
• Vegetables
• Dairy products
• Legumes
• Sweeteners 

There are usually three phases to the diet: 

1. To reduce symptoms, high-FODMAP foods are eliminated from the diet. 
2. FODMAP groups are reintroduced one at a time to identify specific triggers and determine tolerance levels. 
3. The patient enjoys a more varied diet while avoiding symptom triggers during the maintenance phase, where the diet is adjusted based on their tolerance to specific FODMAPs. 

Because the low FODMAP diet can be restrictive and challenging to follow, it is best implemented under the guidance of a healthcare provider or registered dietitian.

Some people find that certain natural remedies may help ease bloating and digestive discomfort associated with slowed digestion or gut irritation. While research on these remedies is still limited, ingredients such as peppermint, ginger, chamomile, and cloves are commonly used to support digestion and reduce feelings of fullness or gas.



Others may use digestive support strategies like diluted apple cider vinegar before meals or activated charcoal supplements to help manage occasional bloating. Because supplements and herbal remedies can interact with medications or may not be appropriate for everyone, it is important to speak with a healthcare provider before adding them to your routine.

Some people explore complementary and alternative therapies alongside conventional treatment to help manage digestive discomfort associated with Hashimoto’s disease. While results can vary from person to person, certain therapies may help support digestion, reduce stress, and improve overall well-being.

Some commonly used approaches include:

• Acupuncture: This traditional therapy uses thin needles placed at specific points on the body and may help some individuals manage pain, stress, and digestive symptoms.
• Digestive enzymes: Digestive enzyme supplements may support the breakdown of food and help reduce bloating or feelings of fullness after meals.
• Mind-body practices: Techniques such as yoga, meditation, breathwork, and mindfulness may help regulate stress, which can sometimes worsen gastrointestinal symptoms.

Because alternative therapies may not be appropriate for everyone, it is important to discuss new treatments or supplements with a healthcare provider before starting them. Working with a qualified practitioner may also help ensure these therapies are used safely and effectively when addressing Hashimoto’s and stomach pain.

Persistent stomach pain, bloating, acid reflux, and digestive discomfort should not be ignored, especially when they may be connected to underlying thyroid or autoimmune issues. Left unaddressed, chronic digestive symptoms can affect nutrient absorption, energy levels, quality of life, and overall well-being.

At HealthierU, we offer comprehensive, personalized, natural treatment for hypothyroidism by looking beyond symptoms alone. We’ll work to identify potential contributing factors such as inflammation, food sensitivities, gut health imbalances, hormone dysfunction, and lifestyle stressors that may be affecting both thyroid function and digestion.

Whether your stomach pain is directly related to Hashimoto’s disease or another gastrointestinal condition, we create individualized treatment plans designed to support long-term healing and whole-body wellness. Through functional and integrative care strategies, our goal is to help you better manage symptoms, improve digestive health, and support optimal thyroid function naturally.

If you are struggling with ongoing stomach pain or digestive symptoms, Dr. Donna Sergi at HealthierU is here to help.

Contact us today to learn more about our personalized approach to Hashimoto’s and digestive health support.