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Reviewed by Yesha Karmeli, naturopathic practitioner (Heilpraktiker) and founder of ORY · Last updated 16.10.2026

A headache in the morning, a sore back after moving house, period pain: for many people an ibuprofen tablet is as routine as a glass of water. But what does ibuprofen actually do to the gut if you take it often – and does the same apply to diclofenac or aspirin?

It is well known that these painkillers can irritate the stomach. Less well known is that they can also affect the small intestine, the gut lining and the gut flora. Here you will read what research knows about this, how problems may show and how the gut barrier can be tested.

At a glance

  • What it's about: Ibuprofen, diclofenac or aspirin are quickly taken. What do they do to the gut lining and gut flora if you take them often?
  • Possible causes: These painkillers inhibit protective prostaglandins and can damage the lining of the small intestine too; they also change the gut flora. The risk rises with dose, duration, age and combinations of several drugs.
  • What you can do: Have black stools, blood in the stool, vomiting blood or severe abdominal pain checked by a doctor immediately; discuss painkillers and stomach protection with your doctor. Do not stop a prescribed medication without talking to your doctor first.
  • What can be measured: Stool markers such as zonulin, calprotectin, alpha-1-antitrypsin and secretory IgA, together with a note of the painkillers you have taken – as building blocks, not a diagnosis.

Person on a sofa with a hand on the back, a glass of water beside them

Ibuprofen and the gut: what happens in the body

Ibuprofen, diclofenac, naproxen and acetylsalicylic acid (aspirin) belong to the non-steroidal anti-inflammatory drugs, NSAIDs for short. They block the enzymes COX-1 and COX-2 and thus the formation of prostaglandins. This relieves pain and inflammation.

But prostaglandins also have a protective role: they support blood flow to the lining and mucus production. In addition, the drugs act directly on the cells of the lining. A review in the journal Gastroenterology describes how this can damage the lining of the stomach and also of the small and large intestine (PubMed 29221664).

Ibuprofen and the gut lining: what you may lose

In the small intestine, specialists speak of NSAID enteropathy. The permeability of the gut wall can increase, bacteria and their components come into closer contact with the lining, and small areas of inflammation, erosions or ulcers can develop (PubMed 29221664).

A capsule endoscopy study showed how common this is: 71 percent of people who took NSAIDs regularly over a longer period had visible changes in the small-intestinal lining, compared with 10 percent in the control group (PubMed 15645405). Many of these cause no symptoms. Another review points out that such small-bowel damage is easily overlooked in everyday practice – for example when it only shows as slow blood loss and anaemia (PubMed 31720893).

Low-dose aspirin, as prescribed to prevent heart attack and stroke, can also affect the small and large intestine (PubMed 26369683).

Ibuprofen and gut flora: what is known about the microbiome

Painkillers do not only act on the lining. In one study, the gut flora of people taking NSAIDs differed, depending on the drug, from that of people not taking them (PubMed 26482265). A review describes a two-way interaction: NSAIDs change the composition of the microbiome, and gut bacteria in turn influence how the drugs are metabolised in the gut and how much they burden the lining (PubMed 32848762).

Laboratory studies also show that many drugs that are not antibiotics at all can inhibit the growth of individual gut bacteria (PubMed 29555994). How much this matters in an individual case cannot be read from these studies.

Calm wooden shelf with a linen towel, a glass of water and a plant

Ibuprofen and gut problems: possible signs

NSAID enteropathy often causes no symptoms (PubMed 31720893). Possible signs are abdominal pain, bloating, diarrhoea or anaemia, which can show as tiredness and pallor (PubMed 29221664). These complaints have many causes, however, and do not allow self-diagnosis.

Seek medical advice immediately if you have black, tarry stools, blood in your stool, vomit blood or have severe abdominal pain. These can be signs of bleeding in the gastrointestinal tract.

Who is particularly affected

The risk of damage to the gastrointestinal tract increases with dose and duration, with age and when several drugs are combined, for example NSAIDs together with aspirin, cortisone or blood thinners (PubMed 29221664).

A proton pump inhibitor such as pantoprazole is often prescribed to protect the stomach. It protects the stomach, but not the small intestine. In animal studies, proton pump inhibitors even increased NSAID damage in the small intestine, probably via changes in the gut flora (PubMed 21745447). Whether this applies to the same extent in humans has not been conclusively established. So do not change anything on your own, but talk to your doctor about it.

Measure instead of guessing: testing gut barrier and inflammation

Whether the gut lining is irritated or the gut barrier more permeable cannot be read from symptoms. Stool markers can give clues. The gut barrier & absorption test measures, among other things, zonulin, calprotectin, alpha-1-antitrypsin and secretory IgA, as well as values for digestion and nutrient absorption. More on nutrient absorption in the gut is covered in Nutrients not being absorbed?

Important for interpretation: calprotectin is an inflammation marker in stool, and it is often raised in people who take NSAIDs regularly (PubMed 10446103). So always state which painkillers you have taken in recent weeks. An abnormal value is a reason to talk to a doctor, not a diagnosis.

What to discuss with professionals

Do not stop a prescribed medication without talking to your doctor first. This applies especially to aspirin prescribed to prevent heart attack or stroke. These questions can help in the conversation:

  • How often and for how long do I actually take painkillers – including over-the-counter ones?
  • Are there other treatment options for my complaints?
  • Is stomach protection useful for me, and does it also protect the gut?
  • Should my blood count or iron levels be checked?

The ORY expert team can also help you interpret a stool result.

In short

  • Ibuprofen, diclofenac and aspirin block protective prostaglandins and can affect the lining not only of the stomach but also of the small intestine (PubMed 29221664).
  • Many long-term users show changes in the small-intestinal lining, often without symptoms (PubMed 15645405).
  • NSAIDs interact with the gut flora (PubMed 32848762).
  • Stomach protection protects the stomach, not automatically the small intestine (PubMed 21745447).
  • Stool markers for the gut barrier give clues; always state your painkiller use, as it can raise calprotectin (PubMed 10446103).

Person writing down questions for a doctor appointment at a wooden desk

Frequently asked questions

Does ibuprofen damage the gut?

Ibuprofen can affect the lining of the stomach and small intestine, especially when taken regularly over a longer period (PubMed 29221664). An occasional tablet is different for most people from continuous use.

Does ibuprofen harm gut flora?

Studies show that the gut flora of people taking NSAIDs can change – differently depending on the drug (PubMed 26482265) (PubMed 32848762). How important this is for an individual’s health has not yet been sufficiently researched.

What are the side effects of ibuprofen on the gut?

Possible effects include increased permeability of the gut wall, small areas of inflammation, erosions and ulcers in the small intestine, and blood loss that can lead to anaemia (PubMed 29221664) (PubMed 31720893). Many changes cause no symptoms.

Can ibuprofen damage the gut lining?

Yes, this is well documented. In a capsule endoscopy study, 71 percent of long-term users had visible changes in the small-intestinal lining (PubMed 15645405).

Diclofenac and the gut: does the same apply?

Like ibuprofen, diclofenac is an NSAID and works through the same mechanism. The risks described for the stomach and gut therefore apply to the group as a whole, although to different degrees depending on drug and dose (PubMed 29221664).

Can ibuprofen cause long-term damage to the gut?

With long-term use, ulcers and in rare cases narrowings can develop in the small intestine (PubMed 31720893). If you need painkillers permanently, discuss this regularly with your doctor.

Does aspirin affect the gut in the same way?

Low-dose aspirin can also affect the small and large intestine (PubMed 26369683). If it was prescribed to prevent heart attack or stroke, do not stop it on your own.

Important note: This article does not replace medical advice, diagnosis or treatment. It is for general information only. If your symptoms are persistent or severe, please contact your doctor. Do not stop a prescribed medication without talking to your doctor first.

Sources

  1. Bjarnason I et al. Mechanisms of Damage to the Gastrointestinal Tract From Nonsteroidal Anti-Inflammatory Drugs. Gastroenterology. 2018. PubMed 29221664
  2. Graham DY et al. Visible small-intestinal mucosal injury in chronic NSAID users. Clin Gastroenterol Hepatol. 2005. PubMed 15645405
  3. Scarpignato C et al. Drug-Induced Small Bowel Injury: a Challenging and Often Forgotten Clinical Condition. Curr Gastroenterol Rep. 2019. PubMed 31720893
  4. Pavlidis P, Bjarnason I. Aspirin Induced Adverse Effects on the Small and Large Intestine. Curr Pharm Des. 2015. PubMed 26369683
  5. Rogers MAM, Aronoff DM. The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clin Microbiol Infect. 2016. PubMed 26482265
  6. Maseda D, Ricciotti E. NSAID-Gut Microbiota Interactions. Front Pharmacol. 2020. PubMed 32848762
  7. Maier L et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. 2018. PubMed 29555994
  8. Wallace JL et al. Proton pump inhibitors exacerbate NSAID-induced small intestinal injury by inducing dysbiosis. Gastroenterology. 2011. PubMed 21745447
  9. Tibble JA et al. High prevalence of NSAID enteropathy as shown by a simple faecal test. Gut. 1999. PubMed 10446103