Probiotic side effects: what is common, what fades, and who should ask a doctor first

The short list

• Gas comes first on the lists: in healthy people, "probiotics may cause gas," NIH's Office of Dietary Supplements says, and Cleveland Clinic writes that the added bloating and gas "should resolve within a few days."^1,5
• Short-term diarrhea, constipation or stomach pain can come with a new probiotic too, Cleveland Clinic says, more often when the dose is large or the gut tends to be sensitive.⁵
• Bacteria or fungi in the blood, and infections serious enough to cause severe illness, have been tied to probiotics in a few cases, nearly all in people who were very sick or immune-weakened.²
• In October 2023, FDA warned that preterm infants given probiotic products are at risk of invasive, potentially fatal disease or infection.⁴
• Of 384 trials of probiotics, prebiotics and synbiotics published from 2015 to 2018, 106 reported no harms data and 309 did not give serious adverse events per group.⁷

How long do probiotic side effects last?

Usually days, not weeks. Cleveland Clinic writes that the added bloating and gas "should resolve within a few days," and describes loose stools from a new probiotic as temporary. No source we checked gives a day count for looser or harder stools, so this site's guides use agency limits for when to call a doctor instead. A reaction that worries you is not something to wait out.⁵

The time frame for early gas is in gas in the first weeks of a probiotic, the point to call a doctor about loose stools is in can probiotics cause diarrhea or loose stools?, and the one for harder stools is in can probiotics cause constipation?

How often do probiotics cause side effects?

Nobody can say precisely, because trials often leave side effects out. A 2018 review of 384 trials of probiotics, prebiotics and synbiotics, published from 2015 to 2018, found that 106 (28%) reported no harms data at all, and 309 (80%) did not give the number of serious adverse events in each group. Its authors wrote that safety cannot be broadly concluded without the data.⁷

"We cannot broadly conclude that these interventions are safe without reporting safety data."

Bafeta and colleagues, Annals of Internal Medicine, 2018

A 2015 review in Clinical Infectious Diseases says the same of the wider record: "Safety outcomes are inconsistently reported in published clinical trials." It also quotes a 2011 report by a US federal research agency, which found no evidence of increased risk in the trials but concluded that "the current literature is not well equipped to answer questions on the safety of probiotics in intervention studies with confidence."⁸

Where trials did report them, the probiotic and placebo groups looked alike. In the trials behind the British Dietetic Association's 2025 constipation guidelines, adverse events, gut symptoms included, showed up in both probiotic and placebo groups, "the number of events was similar between groups," and few studies reported them at all.⁹

Can probiotics cause serious side effects?

Rarely, and mostly in people who are already very ill. NIH's health professional fact sheet ties probiotics to a few cases of bacteremia and fungemia, meaning bacteria or fungi in the blood, and to infections that caused severe illness; most of those patients were severely ill or immunocompromised. FDA has warned that preterm infants given probiotic products are at risk of invasive, potentially fatal disease. NCCIH adds risks that come from the product itself.^2,4,3

The yeast cases show who is at risk. NIH counts "at least 60 reports" since 1966 of fungal blood infections tied to probiotics made with the yeast Saccharomyces cerevisiae; in many, the patients were in intensive care, fed by tube or through a vein, had a central venous catheter, or had received broad-spectrum antimicrobial drugs.² For preterm babies, FDA said in October 2023 that probiotic products used in hospitals had contributed to invasive disease, including one infant death that year, and had been tied to more than two dozen other reported adverse events in the United States since 2018.⁴

NCCIH lists the possible harms as "infections, production of harmful substances by the probiotic microorganisms, and transfer of antibiotic resistance genes from probiotic microorganisms to other microorganisms in the digestive tract," and notes that some products have been found to contain microorganisms not on the label.³ Cleveland Clinic puts the contamination risk in proportion: "This is rare, and it's not a serious risk for most people," though in a weakened immune system it could cause a serious infection.⁵

A 2023 safety review by a panel convened by ISAPP, a scientific association on probiotics and prebiotics (its members include employees of probiotic and food companies), concluded that established practices are sensibly addressing safety for traditional probiotics in the general population, while asking for more rigor in reporting adverse events.¹⁰

Who should ask a doctor before taking a probiotic?

People who are seriously ill, have a weakened immune system or take immune-suppressing medicine, parents of a premature baby, and anyone pregnant or breastfeeding. In NIH's words, probiotics "might not be safe for everyone," and NCCIH says to talk with your health care provider first, especially if you have health problems. Cleveland Clinic names people on immunosuppressant drugs, people with critical illnesses and premature babies as having a small risk of adverse side effects.^1,3,5

• Seriously ill, or in hospital. "Probiotics might also cause problems such as bacterial infections in people who are already seriously ill or who have weak immune systems." (NIH)¹
• A weakened immune system, including from medicine. Cleveland Clinic includes people taking immunosuppressant drugs among those with a small risk of adverse side effects.⁵
• A premature baby. "The FDA has reported that probiotics might cause infections or even life-threatening illness in preterm infants." (NIH)¹
• Anyone with health problems. "If you're considering a probiotic dietary supplement, consult your health care provider first. This is especially important if you have health problems." (NCCIH)³

Physician's Choice's own wording on pregnancy, allergies and reactions is below. Its page of side effects listed for Physician's Choice products uses the same wording.¹¹

Can probiotics interact with medicines?

Two pairings come up in the sources. Cleveland Clinic counts people taking immunosuppressant drugs among those with a small risk of adverse side effects. With antibiotics, NCCIH's summary of a 2017 analysis says the combination appears safe except for people who are very weak or have poorly working immune systems. A 2023 expert safety review lists interactions with drugs among the questions research still has to answer.^5,3,10

That line comes from an analysis of 31 studies (8,672 patients, most in hospital) in which people took probiotics with antibiotics: "the use of probiotics along with antibiotics appears to be safe, except for patients who are very weak or have poorly functioning immune systems."³ Timing a probiotic around an antibiotic is a question for your pharmacist.

The short version

For healthy people, the side effects of a probiotic are mostly mild gas and bloating that settle within a few days, with short-term changes in stools possible at a large dose. Serious infections are rare and cluster in people who are severely ill, immune-weakened or born preterm, and those groups should ask a doctor first. Trials often fail to report side effects, so how common they are is not well measured.