Why You're Always Clearing Your Throat (Meet Pepsin, the Enzyme Behind Silent Reflux)

Short answer: If you clear your throat all day and the allergy pills, nasal sprays, and humidifier have done nothing, the likely driver is pepsin. Pepsin is a stomach enzyme that travels up with reflux, binds to throat tissue, and can be switched back on by acid long after the reflux event is over. This is the hallmark of LPR (silent reflux), and it explains why treatments built for heartburn so often miss it.

You've Been Told it's Allergies. It Probably Isn't.

I hear this in almost every LPR intake. Dozens of throat clears a day. A lump that never quite goes away. A dry cough, or a voice that's hoarse by 3pm. You've done the antihistamines, the saline rinse, the humidifier by the bed, and nothing has touched it.

If that's you, you're not imagining it. Throat clearing is one of the most common symptoms of reflux you cannot feel, and the reason it lingers has less to do with acid than with an enzyme called pepsin.

What Pepsin Actually Is

Pepsin is the enzyme your stomach makes to break down protein. Inside the stomach, it's doing exactly the job it was built for, in an environment built to handle it.

The trouble starts when reflux carries pepsin up past the esophagus and into your throat and voice box. That tissue has none of the stomach's protection. Pepsin lands on it, and the cells there actually pull it inside. Research from Nikki Johnston's lab at the Medical College of Wisconsin showed that laryngeal cells take up pepsin through receptor-mediated endocytosis, meaning the tissue absorbs the enzyme rather than simply being splashed by it (Johnston et al., 2007, Annals of Otology, Rhinology & Laryngology, PMID: 18217514, DOI).

Once pepsin is bound to your throat tissue, it depletes the protective proteins that lining relies on. That is the irritation you feel as the tickle, the lump, and the constant need to clear.

Why Your Symptoms Feel Constant and Random at The Same Time

This is the piece that changes how most of my clients understand their body.

Pepsin does not wash away when the reflux event ends. In a lab study on human pepsin, the enzyme stayed stable for at least 24 hours at a neutral pH of 7, and kept 79% of its activity once the pH dropped back down to 3 (Johnston et al., 2007, The Laryngoscope, PMID: 17417109, DOI). The average pH of your throat sits around 6.8, so the pepsin parked there is dormant, waiting. An acidic reflux event, or something acidic you sip or eat, can switch it back on.

So one reflux event overnight can set up a throat that reacts to coffee at 8am, tomato sauce at noon, and sparkling water at 4pm. That pattern has a mechanism, and once you see it, the randomness disappears.

It also explains why treating each symptom on its own never seems to add up. The cough drop, the allergy pill, and the throat spray all address the surface. Underneath, they share one root contributor.

LPR vs. GERD: Why Your Endoscopy Came Back Normal

With classic GERD, you usually feel heartburn, and an endoscopy may show visible changes in the esophagus. LPR, laryngopharyngeal reflux, works differently. The refluxate travels higher, into the throat and voice box, often without the burning you'd expect. The tissue up there is far more sensitive than the esophagus, so it takes much less exposure to cause symptoms, and it frequently leaves none of the esophageal damage a standard scope is looking for.

So the scope comes back clean, and you leave the appointment wondering if it's all in your head. It isn't. You're dealing with a mechanism the standard workup was never designed to catch.

What Actually Helps

If your plan has become a longer and longer list of foods to avoid, restriction alone does not soothe tissue that's already irritated, and it does not change how often pepsin reaches your throat in the first place.

The work is a healing architecture: strategic additions that support the barrier and calm the tissue, alongside habits that reduce reflux events. Here is what I teach my clients, in the order we usually build it.

• The 3-Hour Buffer: stop eating 3 hours before bed. Beverages are fine. Nighttime reflux is where a lot of pepsin gets deposited, because you're lying flat and swallowing less, so this one change cuts off the biggest supply line.

• The LES Lock: 1 to 5 minutes of diaphragmatic breathing with 360 ribcage expansion immediately after meals, up to 5x daily. This strengthens the crural diaphragm, the muscle wrapped around your lower esophageal sphincter (LES), and raises the pressure that keeps stomach contents down. These bite-size practices are achievable, and consistency is the secret sauce.

• Soluble fiber, used strategically: In a 16-week prospective randomized trial of 505 patients with confirmed LPR, adding psyllium husk to PPI therapy produced an 82% symptom resolution rate, compared with 65% on the PPI alone, and the psyllium group improved fastest (Rana et al., 2025, Indian Journal of Otolaryngology and Head and Neck Surgery, PMID: 40226240, DOI). A separate trial in non-erosive GERD found that 10 days of psyllium raised minimal resting LES pressure and cut the number of reflux events from about 68 to 42 (Morozov et al., 2018, World Journal of Gastroenterology, n=30, PMID: 29881238, DOI). Fewer reflux events means less pepsin reaching your throat and less time in contact with it.

• Mucosal soothing for the tissue itself: Mucilaginous herbs like slippery elm coat and soothe on the way down, and DGL and zinc carnosine support healthy mucosal tissue. This is the piece most protocols skip entirely.

• Nervous system regulation: Stress shifts your body out of rest-and-digest, slows gastric emptying, and loosens LES coordination. Longer exhales and hand-on-belly breathing before meals are simple entry points.

Small hinges swing big doors. You don't need to fear every meal. You need support in the right places.

Once your throat clearing stops feeling random, you can finally build a plan that targets the actual driver instead of chasing the symptom. If you want to go deeper on LPR, start here:

Related reading on mollypelletier.com:

• Acid Reflux vs GERD vs LPR: Understanding the Differences Between the Diagnoses

• The Complete LPR & Silent Reflux Natural Treatment Guide: A Dietitian's Evidence-Based Approach

If your throat and esophageal tissue need soothing support, Sequoia Soothe is the formula I built for exactly that, with slippery elm (1,000mg per serving), L-glutamine, DGL, and zinc carnosine to soothe irritated tissue and support esophageal health. And if you're ready for a personalized plan, applications to work 1:1 with our expert team of reflux Dietitians are open atmollypelletier.com/acid-reflux-specialist.

With love,

Molly Pelletier, MS, RD