Persistent stomach pain that won’t go away typically falls into one of several categories: a functional disorder (where the gut is extra sensitive but structurally normal), an inflammatory condition, an infection, or a reaction to something you’re eating or taking. Clinically, abdominal pain counts as “chronic” when it lasts at least three months, whether it’s constant or comes and goes. If that timeline sounds familiar, you’re far from alone. Functional digestive pain affects roughly one in every 23 to 51 people, depending on the type.
Where It Hurts Narrows the List
Your abdomen contains different organs in different zones, and paying attention to where your pain concentrates can point toward a cause. Upper-center pain (just below the ribs) most often involves the stomach itself, the first part of the small intestine, or the pancreas. Pain in the upper right may involve the liver or gallbladder. Lower right pain raises the question of the appendix or, in people with female reproductive organs, the right ovary. Lower left pain often relates to the descending colon or sigmoid colon.
That said, gut pain is notoriously hard to pin down. It can radiate, shift, or feel diffuse across the whole belly. Location is a useful starting clue, not a diagnosis.
Irritable Bowel Syndrome (IBS)
IBS is the most common explanation for ongoing stomach pain with no visible damage to the gut. The diagnostic standard requires recurring abdominal pain at least one day per week for the last three months, with symptoms first appearing at least six months earlier. The pain also needs to be linked to at least two of the following: it changes when you have a bowel movement, it comes with a shift in how often you go, or it comes with a shift in the consistency of your stool.
If a doctor were to look at the colon of someone with IBS using a scope or imaging, everything would appear normal. There’s no inflammation, no ulcers, no structural damage. The problem is functional, meaning the gut’s muscle contractions aren’t coordinating properly and the nerve endings lining the bowel are unusually sensitive. Researchers now believe this is fundamentally a communication problem between the brain and the gut rather than an issue in the digestive tract alone.
IBS symptoms tend to flare after large meals or during periods of stress, and they’re often temporarily relieved by a bowel movement. That pattern is one of the clearest distinguishing features.
Functional Dyspepsia
If your pain sits high in the abdomen and is more about burning, bloating, or feeling uncomfortably full after eating, functional dyspepsia is a likely explanation. It presents in two main ways. The first is an aching or burning sensation in the upper stomach area, similar to heartburn, that doesn’t necessarily follow meals. The second is postprandial distress, where you feel stuffed or bloated after eating even a normal-sized meal, sometimes with nausea or excessive belching.
Like IBS, functional dyspepsia doesn’t show up on scans or scopes. The organs look fine. The discomfort comes from how the nerves in the digestive tract process normal signals like stretching, acid, and movement.
Why Your Nerves May Be Overreacting
A concept called visceral hypersensitivity underlies many cases of chronic stomach pain. Normally, your gut sends signals to your brain as food moves through, and you don’t consciously feel most of them. In visceral hypersensitivity, those nerves become dialed up so that ordinary sensations like the stomach expanding after a meal register as pain.
This heightened sensitivity often develops after a specific triggering event: a severe stomach infection, a period of intense stress, or an injury that caused acute inflammation. After the original problem resolves, the nervous system stays stuck in a hyper-reactive state, continuing to interpret normal gut activity as a threat. The pain signals travel not only to the brain region that registers physical pain but also to areas that process emotion, which is why chronic stomach pain and anxiety so often feed each other.
Infections That Cause Lasting Pain
H. pylori is a bacterial infection that lives in the stomach lining and is one of the most overlooked causes of persistent upper abdominal pain. It produces an aching or burning sensation that often feels worse when the stomach is empty and improves temporarily after eating. Left untreated, H. pylori can lead to peptic ulcers. Testing is straightforward, usually a breath test or stool test, and treatment is a short course of antibiotics.
If your pain has a burning, hunger-like quality that wakes you at night or peaks between meals, this infection is worth ruling out specifically.
Inflammatory Bowel Disease
Inflammatory bowel disease (IBD), which includes Crohn’s disease and ulcerative colitis, is fundamentally different from IBS despite the similar-sounding names. IBD causes actual, visible inflammation and can permanently damage the intestinal lining. Doctors can see it on imaging and biopsy. IBS cannot be seen on any test.
The distinguishing symptoms of IBD include bleeding (blood in stool or rectal bleeding), unintended weight loss, fever, and anemia. IBS does not cause any of these. If your chronic stomach pain comes with weight you can’t explain losing, bloody stool, or fevers, those point toward IBD or another inflammatory condition rather than a functional disorder.
Celiac Disease
Celiac disease is an autoimmune reaction to gluten that damages the lining of the small intestine. It can cause chronic abdominal pain, bloating, diarrhea, and fatigue, but it can also present subtly with vague, persistent discomfort that’s easy to dismiss. Screening involves a blood test that measures specific antibodies, which is highly accurate as long as you’re still eating gluten when tested. If you’ve already cut gluten from your diet before testing, the blood work may come back falsely negative, and genetic testing becomes the better first step.
Because the intestinal damage in celiac disease can be patchy rather than uniform, a biopsy typically requires samples from four or more sites to avoid missing it.
Pain Relievers That Cause Stomach Pain
Common over-the-counter anti-inflammatory drugs like ibuprofen and naproxen are a frequent and underappreciated cause of chronic stomach discomfort. Up to 40% of regular users report mild upper digestive symptoms. These drugs work by blocking an enzyme involved in inflammation, but that same enzyme helps maintain the protective mucus lining of the stomach. Without that protection, stomach acid can erode the tissue directly.
The damage happens in stages. Early on, it’s superficial irritation and dyspepsia. With prolonged or high-dose use, it can progress to silent ulcers (ones that don’t cause obvious symptoms until they bleed) or, in serious cases, perforation. If you take these medications regularly for headaches, back pain, or joint pain, they may be the very reason your stomach hurts.
Food Triggers and the Low FODMAP Approach
For pain that’s clearly tied to eating, a structured elimination diet can identify triggers. The most evidence-backed approach is the low FODMAP diet, which temporarily removes certain fermentable carbohydrates found in foods like onions, garlic, wheat, dairy, apples, and beans. These carbohydrates draw water into the intestine and ferment rapidly, producing gas that stretches the gut wall. In someone with visceral hypersensitivity, that stretch becomes pain.
Research at Johns Hopkins has found that a low FODMAP elimination diet reduces symptoms in up to 86% of people. The elimination phase is meant to last only two to six weeks before you begin systematically reintroducing foods to identify which specific ones cause problems. It’s not meant to be a permanent diet, and working with a dietitian makes the process significantly more effective.
Symptoms That Need Urgent Attention
Most chronic stomach pain turns out to be functional or manageable, but certain symptoms signal something more serious. Vomiting blood, black or bloody stool, blood in your urine, a swollen and tender abdomen, high fever, persistent vomiting, or pain accompanied by chest tightness and shortness of breath all warrant emergency evaluation. Unintended weight loss, worsening pain at night that disrupts sleep, and new onset of symptoms after age 50 are also red flags that shift the diagnostic approach toward ruling out structural disease.