Where Is Pepsin Located in the Body?

Pepsin is produced and primarily active in the stomach, where specialized cells in the gastric lining release its inactive precursor, pepsinogen, into the stomach’s acidic interior. But pepsin’s story does not end there. Through reflux, aspiration, and even bloodstream absorption, this protein-digesting enzyme turns up in the esophagus, throat, lungs, middle ear, saliva, and urine. Its presence outside the stomach is far from trivial and has reshaped how researchers think about conditions from chronic heartburn to childhood ear infections.

The Stomach Is Home Base

Pepsin begins life as pepsinogen, an inactive molecule synthesized and stored inside chief cells that line the stomach’s gastric glands. When chief cells receive the right signals, they secrete pepsinogen into the stomach cavity. Research on isolated rabbit and human gastric glands has confirmed that these glands synthesize pepsinogen from scratch, building the molecule from amino acids on site rather than importing it from elsewhere.¹ Once pepsinogen hits the highly acidic stomach fluid, the low pH clips off a small segment of the molecule, converting it into active pepsin. This activated enzyme then goes to work breaking down dietary proteins into smaller fragments that the intestines can absorb.

Pepsin works best at a pH around 1.5 to 2.5, which matches the normal acidity of stomach juice during digestion. At a more neutral pH, pepsin loses its cutting ability. But as we will see, “loses” and “destroyed” are very different things.

How the Stomach Avoids Digesting Itself

If pepsin is powerful enough to break apart meat and egg proteins, the obvious question is why it does not eat through the stomach wall. The answer lies in a two-part defense system. The stomach lining secretes a continuous layer of thick mucus gel that physically blocks pepsin from reaching the cells underneath. Embedded in that mucus, bicarbonate ions create a pH gradient: the surface nearest the stomach cavity is acidic, but the surface touching the actual tissue stays close to neutral. Because pepsin is inactive at near-neutral pH, any enzyme that does creep through the mucus loses its bite before it contacts living cells.² Under normal conditions this barrier is enough to keep both the stomach and the upper duodenum safe.

When this defense breaks down, pepsin becomes part of the problem rather than the solution. Ulcers, certain medications, and bacterial infections like H. pylori can thin the mucus layer or disrupt bicarbonate secretion, allowing acid and pepsin direct access to vulnerable tissue. That is one reason peptic ulcers carry the enzyme’s name.

The Esophagus and Reflux Disease

During an episode of gastroesophageal reflux, stomach contents splash upward past the lower esophageal sphincter. That refluxate carries acid, bile salts, and pepsin into the esophagus, a tube whose lining was never designed to handle any of them. Animal studies indicate that the combination of acid and pepsin together inflicts far more damage to esophageal tissue than either one alone.³

Research into how this damage occurs points to pepsin’s ability to break apart the tight junctions between esophageal cells. Once pepsin loosens those cell-to-cell seals, the lining becomes leaky. Acid then seeps through the gaps to reach deeper layers that are even more vulnerable, a process that can convert mild, non-erosive reflux into full-blown erosive esophagitis.⁴ This is an important distinction for people who take acid-suppressing medications and still have symptoms. Reducing stomach acid lowers pepsin’s activity, but pepsin itself may still be present in the refluxate, and as the next sections explain, it does not need full acidity to cause trouble.

Why Pepsin Stays Dangerous Even at Neutral pH

A critical finding that changed how scientists view extra-gastric reflux is that pepsin is surprisingly durable outside its preferred acidic environment. At a pH of 6.5 or higher, pepsin stops cutting proteins. But it does not fall apart. Experiments have shown that pepsin remains structurally intact at pH 7.0 for at least 24 hours at body temperature. If the pH then drops back to 3.0, pepsin snaps back to about 79% of its original activity.⁵ The enzyme is only irreversibly destroyed above pH 8.0.

This matters because many parts of the body that encounter refluxed pepsin sit at a pH between 6 and 7. The throat, for instance, is slightly acidic to neutral. Pepsin that lands there can linger in an inactive but intact form, then reactivate whenever a fresh wave of acidic reflux arrives or even when local pH dips briefly. The practical takeaway is that pepsin does not need to arrive in a bath of stomach acid to eventually do harm.

The Throat and Laryngopharyngeal Reflux

When reflux climbs high enough to reach the throat and voice box, the condition is called laryngopharyngeal reflux, or LPR. Symptoms tend to look nothing like classic heartburn. Chronic throat clearing, hoarseness, a sensation of a lump in the throat, and a persistent cough are more typical. Unlike the esophagus, which has some inherent defenses against brief acid exposure, the laryngeal lining is much more vulnerable.

Pepsin appears to be the central villain in LPR. A 2024 study demonstrated that pepsin triggers an inflammatory cascade in laryngeal tissue by generating reactive oxygen species, which in turn activate a molecular alarm system that produces damaging inflammatory signals.⁶ The higher the pepsin concentration, the more intense the inflammation. In mouse models, drugs that specifically inhibit pepsin reduced laryngeal inflammation and preserved the integrity of the throat lining, providing evidence that pepsin itself, not just acid, drives the damage.⁷

Even more striking is what happens at the cellular level. Laryngeal epithelial cells actively take pepsin inside themselves through a process called receptor-mediated endocytosis, essentially the same mechanism cells use to import nutrients like iron-carrying transferrin.⁸ Once inside, pepsin damages the cell’s mitochondria and Golgi apparatus even when the surrounding environment is at neutral pH.⁹ This intracellular uptake also disrupts the cell’s normal stress-protein response, which is its built-in repair mechanism for coping with acid exposure. The result is a cell that becomes worse at defending itself over time.¹⁰

Pepsin in the Lungs

When reflux or swallowing dysfunction causes stomach contents to enter the airways, pepsin can end up deep in the lungs. Clinicians have used the detection of pepsin in bronchoalveolar lavage fluid, the liquid collected during a bronchoscopy, as a marker for aspiration. In adults hospitalized with pneumonia, elevated pepsin levels in lavage fluid were strongly associated with aspiration as the underlying cause.¹¹ Similar findings appear in children: those with gastroesophageal reflux and chronic cough had significantly elevated pepsin in their lavage fluid compared to controls.¹²

The lung connection carries especially high stakes after organ transplantation. Among lung transplant recipients, over 80% had detectable activated pepsin in at least one lavage sample. Those with detectable pepsin had nearly ten times the odds of developing acute cellular rejection compared to those without it.¹³ Aspiration of gastric contents appears to provoke an immune response in the transplanted lung, making pepsin detection a potential early warning signal for graft problems.

The Middle Ear in Children

One of the more surprising places pepsin has been found is the middle ear. Gastric pepsin has been detected in middle ear fluid from children with otitis media (ear infections with fluid buildup) but not in control patients without ear disease.¹⁴ The proposed route is straightforward: refluxed stomach contents travel up the esophagus, reach the back of the throat, and enter the Eustachian tube, which connects the throat to the middle ear. Because that tube is shorter and more horizontal in young children, they are more susceptible.

Comparisons between children with otitis media and controls found significantly higher concentrations of both pepsin and pepsinogen in the middle ear fluid of the affected group.¹⁵ The role of reflux in ear disease appears to be strongest in younger children and in cases involving thick, pus-like effusions. This does not mean reflux causes all childhood ear infections. Bacterial and viral pathogens are still the major players. But the presence of pepsin suggests that reflux may be an underappreciated contributor in kids with recurrent or stubborn ear fluid.

Pepsin in Saliva as a Diagnostic Tool

Because pepsin travels upward with reflux, it eventually washes into the mouth and mixes with saliva. Researchers have tried to exploit this by using saliva-based pepsin tests as a simple, non-invasive way to diagnose reflux disease. A rapid lateral-flow device called Peptest has been developed for exactly this purpose, detecting pepsin in saliva or sputum samples collected after a reflux episode.¹⁶

The concept is appealing: instead of swallowing a pH probe for 24 hours, you spit into a tube. But the reality is mixed. A meta-analysis pooling results across studies found that salivary pepsin has only moderate diagnostic accuracy for gastroesophageal reflux disease and is not as helpful as initially hoped.¹⁷ One challenge is that healthy people can have trace pepsin in their saliva from normal, non-pathological reflux events, muddying the line between “positive test” and “disease.” That said, salivary pepsin testing did pick up a higher proportion of positive results than traditional 24-hour pH monitoring in patients with non-erosive reflux disease, a notoriously hard-to-diagnose subgroup.¹⁸ So salivary pepsin testing may find its niche not as a standalone diagnostic but as one piece of a larger clinical puzzle, especially when standard tests come up empty.

Pepsinogen in Blood and Urine

Not all pepsinogen stays in the stomach. A small fraction leaks from gastric glands into the bloodstream, where it circulates as plasma pepsinogen. The kidneys eventually filter it out, and it can be measured in urine, where it has historically been called uropepsin. Studies measuring baseline levels of both plasma pepsinogen and urinary pepsinogen in healthy infants and children established that these circulating levels are a normal physiological finding, not a sign of disease.¹⁹

The clinical relevance here has less to do with pepsin’s digestive action and more to do with what blood pepsinogen levels reveal about the stomach itself. Low serum pepsinogen I levels, for example, are widely used in some countries as a screening marker for atrophic gastritis, a condition in which the stomach lining thins and loses its acid-secreting glands. The logic is that as the glands disappear, they produce less pepsinogen, so falling blood levels serve as an indirect window into the stomach’s health without requiring an endoscopy.

Pepsinogen Expression in Cancer

Under normal circumstances, pepsinogen production is largely confined to gastric chief cells. But certain cancers flip on the pepsinogen gene in tissues where it would not normally be active. One form, pepsinogen C, has been found at elevated levels in tumors of the colon, rectum, bladder, breast, and uterus, while being reduced in stomach adenocarcinoma itself.²⁰ Ectopic pepsinogen C expression has also been reported in prostate and ovarian cancers.²¹

In rare cases, the connection between pepsinogen and cancer takes an anatomical form. A subtype of mucin-producing lung cancer was found to mimic the structure of stomach glands so closely that the tumor cells stained positive for pepsinogen II on immunohistochemistry.²² These findings do not mean pepsinogen causes cancer. Rather, cancer cells sometimes reactivate developmental gene programs, and pepsinogen expression is part of that hijacked toolkit. Researchers are investigating whether these ectopic expression patterns could eventually serve as diagnostic markers or therapeutic targets.

Alginates and Other Ways to Neutralize Pepsin

Standard acid-suppressing drugs like proton pump inhibitors reduce the acidity that activates pepsinogen into pepsin, and they do so effectively. But they do not eliminate pepsin that is already active or sitting in the refluxate in a stable, potentially reactivatable form. This gap has led researchers to look at agents that target pepsin directly.

Alginates, compounds derived from seaweed, can reduce pepsin activity in laboratory settings. One study found that the best-performing alginate formulation reduced pepsin activity by about 89% at high concentrations.²³ Complete suppression was not achieved, and the degree of inhibition varied depending on the alginate’s molecular structure. A commercially available alginate suspension was also shown to inhibit pepsin activity in a dose-dependent manner and to physically trap pepsin and bile acids, limiting their ability to diffuse into the esophageal lining.²⁴

For LPR, where pepsin may be the primary aggressor, the pepsin-inhibiting drug pepstatin and the HIV protease inhibitor darunavir (which happens to also inhibit pepsin) have both shown promise in animal models, suppressing laryngeal inflammation and preserving tissue integrity.⁷ These are still experimental approaches, and no pepsin-specific inhibitor is currently prescribed as a standard reflux therapy. But the research highlights a growing consensus that treating reflux disease may eventually mean targeting pepsin alongside acid, not acid alone.

Pepsin Before Birth

Pepsin production begins surprisingly early in human development. Studies of fetal gastric tissue have detected pepsin activity as early as 10 to 13 weeks of gestation. Unlike gastric lipase, which increases steadily over the following weeks and varies by region of the stomach, pepsin activity remained relatively flat across both gestational age and stomach location during the periods studied.²⁵ The functional significance of fetal pepsin is still debated. The fetus swallows amniotic fluid, and some researchers speculate that early pepsin activity plays a role in processing the proteins dissolved in it, though the fetus obviously does not depend on gastric digestion for its nutrition. What is clearer is that the molecular machinery for pepsin production is in place well before birth, meaning the enzyme is one of the earliest digestive tools the human body prepares.