Do hormones cause gut health problems, or do gut health problems cause hormone problems? Or maybe both. Your gut and your hormones are intricately intertwined. Problems with one can cause problems with the other. Let’s look at which hormones affect your gut and how better gut health affects your hormonal health.

Irritable bowel syndrome (IBS), is a common, and in some respects debilitating, condition that is characterized by symptoms that include abdominal pain, bloating, diarrhea and/or constipation.

Which Hormones Affect Your Gut and How?

Which hormones might affect your gut health? Well, there are reproductive hormones (estrogen, testosterone, progesterone, prolactin, DHEAs, etc.), gut hormones (leptin, ghrelin), stress hormones (cortisol) and thyroid hormones. All of these may influence your digestive tract.

Reproductive Hormones and Digestion

Twice as many women as men are affected by irritable bowel syndrome (IBS), suggesting a role for sex hormones in causing or contributing to the development of IBS.

Prolactin

According to some studies, there appears to be an association between increased blood levels of the hormone prolactin and IBS. Prolactin helps women to breastfeed their infants. This hormone can also be increased when one is under stress. One theory as to why this happens is that the increased prolactin levels may cause oversecretion of cholecystokinin, inducing the development of IBS. Cholecystokinin (CCK) is a digestive hormone released when food from your stomach reaches the first part of your small intestine.

Estrogen and Progesterone

Twice as many women as men are affected by irritable bowel syndrome (IBS), suggesting a role for sex hormones in this condition.

Ovarian hormones vary widely throughout a woman’s menstrual cycle. They affect both sensation and movement in your gut in healthy and IBS populations. They can moderate pain by interacting with nerve balancing systems and the emotional system responsible for perceiving pain in your gut. These hormones also modulate your susceptibility and response to stress. Stress is a pivotal factor in IBS occurrence and symptom severity. For instance, estrogen can cause an increased stress response, promoting immune activation and decreasing your gut barrier function.

The Migrating Motor Complex and Hormones

The migrating motor complex, or MMC, is a pulsatile, muscular movement that propels food and waste through your digestive tract. Normal MMC function is a prerequisite for normal gut health. One study that compared the MMC of women at particular points of their menstrual cycle with that of men found that early in the cycle (day 1 of your period to ovulation), the duration of the MMC cycle during sleep was lengthened. The higher the estrogen level, the longer the MMC cycle duration. In the middle of the luteal phase, the MMC cycle duration during sleep was shorter with higher serum progesterone levels and longer with lower progesterone.

Histamine, IBS and Estrogen

Histamine is a chemical that is released by white blood cells known as mast cells. Histamine is responsible for the typical allergy symptoms of sneezing, runny nose, and watery eyes. It has also been implicated in IBS. A study on progesterone and histamine release showed lower histamine release in the presence of progesterone. Mast cells show a high affinity for estradiol (estrogen) receptors and estradiol increases mast cell secretion. Increased mast cell density and activity in the gut may correlate with symptoms of hypersensitivity in the gut.

Your Hormones and Your Microbiome

The composition of your gut flora reflects both your genetics and your lifestyle. It is in a dynamic state of flux depending on stress, diet, sleep, and medication use. Your gut micro-organisms exert both local and systemic effects. A messed-up gut ecology (dysbiosis) could contribute to the risk of developing gut health problems and more systemic health problems. Your gut bacteria can metabolize estrogen and modulate your serum estrogen levels. Conversely, estrogen-like compounds, such as BPA from plastic, may promote the growth of certain kinds (not necessarily good kinds) of gut bacteria.

Testosterone and IBS

One study in young males found that sufferers of IBS, whether constipation-predominant or diarrhea-predominant, had higher levels of testosterone and a hormone-binding protein known as sex hormone-binding globulin (SHBG). Higher SHBG levels may reflect higher testosterone but also higher estrogen and DHT. As mentioned previously, estrogen affects stress response, your microbiome, and the migrating motor complex.

FODMAPs, Gut Hormones and IBS

The density of gut hormone-producing cells is low in IBS patients. This abnormality may be the direct cause of IBS symptoms. A low number of stem cells and low conversion of these cells into hormone-producing cells probably cause this decreased density. Gut bacteria digest fermentable carbohydrates (FODMAPs) into by-products that decrease gut stem cells. A low FODMAP diet or altering the gut bacteria seems to help restore appropriate numbers of gut stem cells.

Leptin

Leptin is a hormone that is released by your fat cells. It signals your brain that you are full and decreases your appetite and food cravings. In obese people, excessive amounts of leptin are excreted by the fat cells, and the brain responds poorly to it. This is known as leptin resistance. The person’s brain doesn’t get the message to stop eating, further compounding their obesity problem.

Giving your digestive tract adequate time between putting food into it allows for better, more thorough digestion. A meal takes 2-4 hours in the stomach to fully digest. Layering more food on top of the food that hasn’t finished digesting leads to a mix of partially digested and whole, undigested food. Not optimal conditions for complete and healthy digestion.

Research on diarrhea-predominant IBS (IBS-D) identified increased leptin in the digestive tract’s lining. The mast cell activation rate in these patients was also increased. The authors speculated that leptin and increased mast cell activation may play a role in IBS-D.

Ghrelin

Ghrelin stimulates your appetite and the release of growth hormones. It is produced in your stomach and small intestine. Small amounts are also released from your pancreas and brain. Ghrelin stimulates your appetite, causing you to digest more food and store more fat. It also appears to help control insulin release and plays a protective role in cardiovascular health. Ghrelin is released in response to stressful situations. This is part of why we reach for food when we feel stressed. Overproduction of ghrelin due to stress means piling more food into your digestive tract than you need. Overeating contributes to poor digestion and IBS symptoms.

Blood levels of ghrelin are higher in patients with IBS-D.

Corticosteroids and Your Gut

Apart from inflammation of the intestinal lining, nerve inflammation is probably involved in the cause of IBS via the “gut-brain” axis. Your gut-brain axis is the connection between your digestive tract, your nervous system, and your brain. This results in altered hormone pathways and changes in the receptor genes for cortisol, cortisone, and corticosterone (collectively known as corticosteroids). This gives rise to an overall pro-inflammatory picture and dysregulated HPA (hypothalamic-pituitary-adrenal) axis and serotonin-related functioning, which could, at least partially, account for the symptoms of IBS.

Your Gut Bacteria and Your Hormones

The bacteria in your gut regulate your estrogen level through the secretion of an enzyme known as β-glucuronidase. This enzyme unpackages estrogen packaged up for excretion, releasing it in its active form. In this way, your gut bacteria, depending on the mix, increase or decrease your estrogen level. Having the right balance of gut bacteria helps to maintain healthy estrogen levels. An alteration in your gut flora and, therefore, your circulating estrogen level may contribute to obesity, metabolic syndrome, endometrial hyperplasia, endometriosis, polycystic ovary syndrome, fertility, cardiovascular disease (CVD) and altered cognitive function.

Thyroid Hormones and IBS

One common symptom of hypothyroidism is constipation. Think of your thyroid like the gas pedal for your car. Your thyroid determines the speed with which everything else runs. If your gut is working slowly, it can be because it isn’t receiving enough gas from your thyroid.

A 2017 study found an association between hypothyroidism, IBS, and an elevated antibody in the blood known as IgG2. Immune reactions to food can precipitate the release of IgG antibodies, which is the basis for our food sensitivity test. If you want to try lowering your IgG antibodies to see if that helps your IBS and thyroid, book an appointment to discuss food sensitivity testing.

The digestive tract manifestations of hypothyroidism are due to reduced movement. Hashimoto’s thyroiditis, an autoimmune disorder that is the most common cause of low thyroid function, may be associated with symptoms that are related to this decreased movement, including difficulty swallowing or heartburn. Indigestion, nausea, or vomiting may be due to delayed stomach emptying.

Slowed movement through the small intestine adds to abdominal discomfort, gas, and bloating in those with bacterial overgrowth (SIBO). Because of an existing autoimmune disorder, there may be additional autoimmune disorders, such as autoimmune gastritis. This reduces stomach acid production, which has implications for adequate digestion. Constipation may result from diminished motility. Grave’s disease or hyperthyroidism is accompanied by normal stomach emptying but with low acid production. The time for food to pass through the digestive tract is accelerated, resulting in diarrhea.

Symptoms usually resolve with treatment of the thyroid disease.

What Can You Do?

As you can see, several possible hormonal health influences on your digestive tract exist. If you are suffering from IBS, constipation, diarrhea, SIBO, bloating, or gas, there may be a hormonal influence on your digestive tract.

Here’s how I can help:

Comprehensive hormone testing, interpreted within the context of what is IDEAL for you, not just based on the “lab ranges” which are not set based on what is optimal for you
Determine the root cause of your gut health problems and address that for better gut health
Testing for and correcting all of the contributing factors to your gut issues: comprehensive stool testing, food sensitivity testing, hormonal health testing

Book an appointment online now

By Dr. Pamela Frank, BSc(Hons), Naturopathic Doctor, updated March 27, 2025

Picture of Toronto Naturopath Doctor Dr. Pamela Frank, Best Naturopath in Toronto many times over — Dr. Pamela Frank, BSc(Hons), Naturopathic Doctor

Dr. Pamela has practiced as a naturopathic doctor in Toronto since 1999. She has received numerous “Best Naturopath in Toronto” awards. She is registered with the College of Naturopaths of Ontario.

Dr. Pamela Frank uses a natural treatment approach that may include acupuncture, herbal medicine, nutrition, diet, vitamins, supplements, and other natural remedies to restore balance and provide long-term resolution to almost any health problem.