Crohn's Disease

Causes & Triggers of Crohn's Disease

Delving into the causes and triggers of Crohn’s disease is a complex endeavor, as there are a wide variety of different genetic, environmental, and lifestyle factors in the mix. But if you’re living with Crohn’s, understanding the causes and triggers of the disease is fundamental to managing it. 

Why? Because knowledge empowers decision-making about how to handle your symptoms and triggers. With time, dedication, and the right approach, you can successfully manage and reduce Crohn’s impact on your life. 

By grasping what might cause or exacerbate your Crohn’s symptoms, you can make more informed choices about your health — or offer meaningful support to someone else who is dealing with the condition. 

In this article, we’ll break down current research into Crohn’s, providing thoughtful insight to help you understand the causes, triggers, and interactions involved in this complex disease. 

Understanding Crohn’s Disease

Crohn’s disease is a chronic inflammatory condition that primarily affects the gastrointestinal (GI) tract. Many people think of it as strictly an intestinal issue, but Crohn’s can affect other organs and isn’t confined to the GI tract. 

Some of the most common symptoms include persistent diarrhea, abdominal pain, fever, rectal bleeding, weight loss, and fatigue. Crohn’s may also cause or worsen other conditions such as arthritis, skin disorders, eye inflammation, and, in rare cases, liver disease. (Source

Over time, the effects of Crohn’s can accumulate. For example, since Crohn’s inhibits the gut’s ability to absorb nutrients, people often experience weight loss and malnutrition that can affect other organs in the body. (Source)

Understanding causes and triggers is paramount as Crohn’s is characterized by flare-ups, during which symptoms increase, and remission, when symptoms are reduced or absent. By learning about the causes and triggers, you can decrease flare-ups and extend periods of remission. 

Immune System Dysfunction in Crohn’s Disease

Crohn’s disease is an inflammatory bowel disease (IBD) influenced by an overactive immune response. The immune system’s role in the disease, however, is highly contested and remains debated among the scientific community. 

John Hopkins Medicine, for example, states quite categorically about Crohn’s, “It is an autoimmune disorder.” In contrast, the Crohn’s and Colitis Foundation defines Crohn’s as an “inflammatory bowel disease that causes chronic inflammation of the gastrointestinal tract” but stops short of labeling it as an autoimmune disorder. (Source, Source)

Websites such as Medical News Today acknowledge the debate, stating, “Crohn’s disease is a form of inflammatory bowel disease (IBD) with a suspected link to an inflammatory immune response. The exact cause of the disease is still unclear.” (Source)

So why the confusion? 

Autoimmune diseases are typically defined by the body attacking its own cells. In contrast, Crohn’s seems to involve an inflammatory immune response affecting bacteria in the GI tract. Normally, the immune system distinguishes between harmful and beneficial or harmless bacteria, targeting only the harmful ones. However, in Crohn's, it appears beneficial bacteria are targeted, resulting in inflammation that contributes to the development of the disease. (Source

Overall, Crohn’s is best understood as a complex and multifactorial disease, and there are many questions to be answered about its exact causes and mechanisms. (Source)

The next section will explore some of Crohn’s likely triggers, ranging from lifestyle to environmental factors. 

Genetic Factors Influencing Crohn’s Disease

Let’s move on to discuss how genetics influences your chances of developing Crohn’s. 

Research has identified multiple genetic indicators linked to an increased risk of developing Crohn’s disease. You might inherit genetic risk from your parents, or the genes could mutate at some point during your birth, growth, and development. It’s essential to keep in mind, though, that genetic risk doesn’t mean you will definitely develop the disease.

Genes involved in the development of Crohn’s primarily affect the immune system, gut barrier integrity, and the body’s interactions with gut microbiome. (Source)

Family Risk of Crohn’s

Having a genetic component means you’re more likely to develop Crohn’s if it runs in your family, particularly if you have a parent or sibling with the disease. If you have a first-degree relative (parent, sibling, or child) diagnosed with Crohn’s, your risk of developing the disease is estimated to be up to 35 times higher than the population risk.​​ (Source)

While the role of genetics is important, environmental triggers, such as diet and lifestyle, also influence the onset and progression of Crohn's. Being genetically predisposed to developing the disease may make you more vulnerable to these other factors. 

Understanding the Causes and Triggers of Crohn’s Disease

Crohn's has intrigued the medical community for years, and there’s still little consensus on the precise triggers, causes, and the difference between triggers and causes. 

Causes are generally understood as the fundamental drivers of the disease, whereas triggers are factors that can precipitate or worsen the symptoms of Crohn's. However, in Crohn’s, triggers and causes frequently overlap and range from genetics and diet to environmental pollution, smoking, stress — virtually anything that can affect the gut. 

Let’s explore the leading potential triggers and causes in detail. 

Birth and Early Life Exposures

The foundation for health is often laid early in life, and this is also true for the potential development of Crohn's. Mode of birth and manner of feeding in infancy may influence an individual's gut microbiome and immune system, affecting their susceptibility to Crohn's. 

For example, a baby’s gut microbiome is “seeded” by exposure to its mother’s microbiota, so that babies born via cesarean section have different gut flora compared to those born vaginally. Because so much of the immune system is centered in the GI tract, studies suggest this may affect immune system development. Similarly, breastfeeding has been shown to support the development of healthy gut microbiota, potentially offering some protection against autoimmune conditions, including Crohn’s. (Source, Source)

While birth and early life are linked to immune system health and function, it’s tricky to estimate how this affects the lifelong risk of developing Crohn’s disease. 

Microbiome-Related Factors

The gut is home to some 100 trillion microorganisms that are not human cells. This community of microbes is known as the gut microbiome, which is a complex ecosystem that affects everything from mental health to immune system response. (Source)

In Crohn’s, a state of imbalance in the gut microbiome, known as dysbiosis, often occurs. Dysbiosis in Crohn's is characterized by decreased diversity, with reduced abundance of “good” bacterial species and an increase in pathogenic “bad” bacteria. The effects of dysbiosis work in both directions — this microbial imbalance can cause inflammation that contributes to Crohn's, and Crohn’s-related inflammation can make dysbiosis worse. (Source)

Dysbiosis and the inflammation that comes with it can eventually disrupt the gut barrier, leading to increased intestinal permeability, or “leaky gut.” A leaky gut means bacteria and their products can cross the gut barrier and leave the intestines, triggering an immune response and inflammation in other parts of the body. (Source)

Dysbiosis also influences the gut's ability to process and absorb nutrients, contributing to malnutrition. (Source)


Closely related to the health of the gut microbiome, dietary habits can affect the chance of developing Crohn’s, as well as either moderate or worsen its effects. 

The modern Western diet, high in processed foods, sugars, and unhealthy fats, is often linked to increased inflammation, potentially aggravating Crohn’s symptoms. These diets also result in a general decrease in healthy gut bacteria. (Source

In contrast, diets rich in fruits, vegetables, and soluble fiber from lentils, oats, or fatty fish, may help reduce inflammation. 

The low FODMAP diet, which involves limiting certain types of carbohydrates that are poorly absorbed in the gut, has been shown to alleviate symptoms in some Crohn’s patients. (Source)


Stress is known to trigger flare-ups in Crohn’s. Research indicates that gut health is linked to mental health, helping to explain the relationship between Crohn’s and stress. (Source)

The relationship between stress and Crohn’s disease can cause a vicious cycle. Stress can exacerbate Crohn’s symptoms, and, in turn, the discomfort caused by these symptoms can lead to increased stress. (Source)

The Hygiene Hypothesis 

There is some evidence that risk of Crohn’s develops in early life in childhood. 

The “hygiene hypothesis” proposes that a lack of exposure to diverse microbes during childhood, more common in urban and perhaps overly clean environments, might lead to an underdeveloped immune system, increasing susceptibility to autoimmune diseases such as Crohn’s. (Source)

Limited exposure to pathogens can result in an immune system that isn’t “trained” to tell the difference between microbes that are harmless and those that can cause harm. This could explain the body’s inappropriate immune reaction to gut bacteria in Crohn’s. 

Antibiotic Usage

Studies have shown a link between excessive antibiotic use and the risk of developing Crohn’s and other autoimmune diseases. One study found that excessive antibiotic usage in childhood, in particular, can increase the risk of developing the disease. (Source)

Antibiotics taken for bacterial infections may also damage or kill beneficial bacteria in the gut, disturbing their natural balance and functionality. This may increase the risk of developing Crohn’s, but the extent to which this occurs is poorly understood. (Source


Smoking has been consistently linked to an increased risk of developing Crohn’s. The chemicals in cigarette smoke are shown to affect the lining of the digestive tract, altering immune responses and increasing intestinal permeability. Moreover, they contribute to inflammation and impair the body’s ability to heal. (Source)

This can lead to an exaggerated immune response against good bacteria, which is a leading feature of Crohn’s. (Source)

Industrial Pollutants

Industrial pollutants are another possible trigger of Crohn’s. Chemicals released into the environment, such as heavy metals, pesticides, and now-banned polychlorinated biphenyls (PCBs), can accumulate in the human body over time. (Source)

These toxins can disrupt the delicate balance of the gut microbiome and the integrity of the intestinal barrier, leading to increased gut permeability and inflammation. This can trigger or worsen the symptoms of Crohn’s. (Source)

Air Pollution

Air pollution has also been implicated as a risk factor for Crohn’s in recent years. Airborne particulate matter and other pollutants can affect gut health either directly, by being ingested, or indirectly through the inflammatory responses pollution triggers in our bodies. (Source)

Studies have shown a correlation between higher levels of air pollution and increased incidence of Crohn’s, especially in urban areas where air pollution is a serious problem. (Source)


Some researchers propose that a viral or bacterial infection may initiate Crohn’s in susceptible individuals. The theory is that an infection could activate the immune system in the intestines, but that after the infection is cleared the immune response doesn’t shut off as it should. This prolonged immune response could lead to the chronic inflammation characteristic of Crohn’s. (Source)​​

Additionally, infections can alter the balance of gut microbiota, which is known to play a role in the immune response and inflammation. (Source)

Hormonal Influences

Hormones, the body's chemical messengers, regulate physiological processes, including immune system function. In the context of Crohn’s, hormonal fluctuations, especially during puberty, pregnancy, or as a result of contraceptive use, can influence disease onset and progression. (Source)

Women also report worsened Crohn’s symptoms during the menstrual cycle, pregnancy, the postpartum period, and after menopause. Understanding these hormonal influences is crucial for managing Crohn’s disease through different life stages. (Source)

Geographic and Socioeconomic Factors

The prevalence and manifestation of Crohn’s varies worldwide, and it’s typically viewed as more common in developed and Western countries, and within urban areas and cities. (Source, Source)

This ties together with some of the above triggers, such as pollution, diet, and stress, which may be higher in urban areas. Despite the pollution often present in urban settings, children growing up in cities often lack exposure to the microbes present in agricultural and natural areas, which may impair development of a robust immune system.

The Bottom Line 

Crohn's disease is complex and multifactorial. It doesn’t have a singular cause or trajectory. The roots and triggers are complex, forming a web of genetic, environmental, lifestyle, and infectious factors. 

Each person’s experience with Crohn’s is unique, shaped by their genetic background, environmental exposures, lifestyle choices, and possibly hormonal fluctuations.

As with all autoimmune diseases, a comprehensive understanding is key. Acknowledging the interplay among Crohn’s possible causes and triggers lays the groundwork for more effective management and, potentially, prevention. 

While this guide offers an extensive overview, it’s important to remember that health is profoundly personal. It’s crucial to consult with health care professionals who can provide individualized advice, guidance, and strategies suited to your specific situation.

At WellTheory, we dedicate ourselves to supporting you in your autoimmune journey. Our expertise in autoimmune diseases positions us to provide valuable insights, advice, and resources tailored to your needs. 

Together, we can navigate the complexities of Crohn’s, ensuring you are well-informed and empowered to make the best decisions for your health.


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