Do Probiotics Have Any Negative Side Effects? A Guide to Potential Risks

October 17, 2025 •

4 min read

While probiotics are considered safe for the vast majority of healthy individuals, some people may experience side effects, most commonly mild and temporary digestive discomfort like gas or bloating. The potential for more serious risks is rare but exists, particularly for those with weakened immune systems.

Quick Summary

This article explores the potential negative side effects associated with probiotics, from common digestive discomforts to rare but serious risks. It also clarifies who should exercise caution when considering probiotic supplements.

Key Points

Mild digestive issues are common: Temporary gas, bloating, and changes in bowel movements can occur as your gut adjusts to new probiotics.
Not all probiotics are created equal: Side effects can vary depending on the specific strain, dosage, and whether it's from a food source or a supplement.
High-risk groups should be cautious: People with weakened immune systems, critical illnesses, or premature infants face a small but serious risk of infection from probiotics.
Check for histamine-producing strains: Certain fermented foods and some probiotic supplements contain biogenic amines that can trigger headaches in sensitive individuals.
Read supplement labels carefully: Allergic reactions are typically caused by other ingredients like dairy or soy, not the probiotic cultures themselves.
Consult a healthcare provider before use: For anyone with underlying health conditions or persistent side effects, medical guidance is necessary to determine the right course of action.

Understanding the Potential Negative Side Effects of Probiotics

Probiotics are living microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Found in fermented foods and dietary supplements, they are widely promoted for their positive impact on gut and immune health. However, like any supplement, they are not without potential downsides. For most healthy people, adverse effects are mild and transient, but a small percentage of the population may face more significant risks.

Common Digestive Side Effects

When you first begin taking probiotics, your gut microbiome undergoes an adjustment period as the new bacterial strains take hold. This can lead to some noticeable, though usually temporary, digestive symptoms. This process is sometimes referred to as the Herxheimer reaction, where a die-off of harmful bacteria can release toxins that cause temporary discomfort.

The First Few Weeks: What to Expect

Gas and Bloating: This is the most frequently reported side effect and is caused by the new bacteria producing gas as they ferment indigestible plant fibers. Starting with a lower dose and increasing gradually can help mitigate this.
Constipation or Diarrhea: Paradoxically, while often used to treat these very symptoms, some people may experience a temporary shift in bowel habits. A sudden change in gut flora can affect bowel motility and cause either looser or more frequent stools or a period of constipation.
Increased Thirst: Users of yeast-based probiotics may notice an increase in thirst as their body adjusts.

These symptoms typically resolve within a few weeks as the gut's ecosystem finds a new balance. If they persist, it's recommended to consult a healthcare professional.

Allergic and Histamine-Related Reactions

Beyond digestive issues, some individuals may experience other reactions related to the ingredients or metabolic byproducts of probiotics.

Headaches Triggered by Amines

Some probiotic-rich foods, such as yogurt, kimchi, and sauerkraut, contain biogenic amines like histamine, tyramine, and tryptamine. These compounds are formed during the fermentation process and can affect the central nervous system, potentially triggering headaches or migraines in sensitive individuals. In such cases, a supplement may be a better option than fermented foods.

Allergic Reactions to Supplement Ingredients

It is rare to be allergic to the probiotic microorganisms themselves. However, many probiotic supplements contain added ingredients that can cause an allergic response.

Common allergens in supplements include:

Dairy or lactose
Soy
Eggs
Gluten

Individuals with food allergies should always read the label carefully to ensure no hidden ingredients could trigger a reaction.

Serious Risks for Vulnerable Populations

For certain high-risk groups, the potential side effects of probiotics can be more severe and are a significant cause for caution.

Increased Risk of Infection

While extremely rare in healthy individuals, the live bacteria or yeast in probiotics can enter the bloodstream and cause systemic infections like sepsis in immunocompromised individuals.

Those at highest risk include:

People with suppressed immune systems (e.g., those on chemotherapy or with HIV/AIDS)
Critically ill patients in the ICU
People with venous catheters or who have undergone recent surgery
Premature infants

In these cases, a doctor's supervision is essential, and often, probiotics are not recommended. The FDA has issued warnings regarding the use of probiotics in premature infants due to fatal infections.

Antibiotic Resistance Gene Transfer

A theoretical risk associated with probiotic bacteria is the transfer of antibiotic-resistant genes to other, potentially harmful, bacteria in the gut. Some probiotic strains naturally possess genes that make them resistant to antibiotics, and while transfer is not a common event, it remains a concern being studied by scientists.

Comparison of Probiotic Side Effects


Side Effect Type	Common & Temporary	Rare & Serious	Recommended Action
Digestive	Gas, bloating, temporary diarrhea, constipation	Bowel ischemia (severe pancreatitis)	Reduce dosage, consult a doctor if persistent
Allergic	Headaches from amines in fermented foods	Full allergic reaction to supplement ingredients (e.g., dairy, soy)	Switch to supplements or avoid specific foods. Read labels carefully.
Infections	Mild skin rashes (rare)	Systemic infection (sepsis) in high-risk individuals	Stop use and consult a doctor immediately if a rash is severe or accompanied by other symptoms.
Metabolic	Brain fog, cognitive issues (related to SIBO)	D-lactic acidosis (rare, short-gut syndrome)	Consult a doctor; may require specialized treatment.

Conclusion

While the vast majority of people can take probiotics without experiencing serious adverse effects, understanding the potential risks is crucial. For most, side effects are limited to mild, temporary digestive discomfort during an initial adjustment period. However, people with compromised immune systems, severe illnesses, or other specific health conditions must exercise extreme caution due to a low but present risk of serious infection. The safety of probiotics is highly dependent on individual health, the specific strain, and the quality of the product. A healthy, fiber-rich diet that supports a diverse gut microbiome is often a safer alternative for general wellness. If you have any serious health concerns, discussing the risks and benefits with a healthcare provider is the safest approach before starting a probiotic regimen.

For more detailed information, consult the National Center for Complementary and Integrative Health (NCCIH) on probiotic safety: Probiotics: Usefulness and Safety | NCCIH.

Frequently Asked Questions

No, mild side effects like gas and bloating during the first few weeks are often a sign that the probiotics are starting to work and that your gut microbiome is adjusting. These effects should subside over time.

Yes, in some people. Certain probiotic-rich fermented foods contain biogenic amines, which can trigger headaches. If you are sensitive to these compounds, choosing a probiotic supplement over fermented foods may be a better option.

People with severely weakened immune systems, those who are critically ill, and premature infants should generally avoid probiotics due to a rare but serious risk of systemic infection. Consult a doctor before use if you fall into these categories.

You should check with your doctor or pharmacist. Some probiotics can help with antibiotic-associated diarrhea, but not all strains are effective, and some may be less effective when taken concurrently with antibiotics.

If mild digestive symptoms last for more than a few weeks or if you experience more severe reactions, stop taking the probiotic and consult a healthcare professional. They can help you determine the cause and explore other options.

While it's unlikely to be dangerous for most healthy people, taking a very large dose may increase the likelihood of experiencing temporary digestive side effects like gas and bloating. More is not always better, and it's best to follow the recommended dosage.

Allergies to the probiotic microorganisms themselves are very rare. However, allergic reactions can occur due to other ingredients in a supplement, such as dairy, soy, or gluten. Always check the product's label for allergens if you have sensitivities.

No, most probiotics sold as dietary supplements are not strictly regulated by the FDA in the same way as medications. This means the manufacturer doesn't need to prove its product is safe or effective before selling it.