Fibromyalgia doesn’t directly cause diarrhea the way a stomach bug does, but digestive problems, including diarrhea, are remarkably common in people with the condition. The connection runs through several overlapping pathways: a disrupted gut-brain communication system, changes in gut bacteria, a high rate of co-occurring irritable bowel syndrome, and even the medications used to treat fibromyalgia itself.
How Common Are Gut Problems in Fibromyalgia?
People with fibromyalgia report significantly more digestive symptoms than the general population. In comparative studies, fibromyalgia patients score higher for bloating, reflux, nausea, and changes in bowel habits than both healthy controls and people with rheumatoid arthritis. About 42% of fibromyalgia patients report constipation, and many cycle between constipation and diarrhea. These symptoms are disruptive enough to measurably reduce quality of life beyond what the pain and fatigue of fibromyalgia already cause.
Perhaps the most telling statistic is how frequently fibromyalgia and irritable bowel syndrome appear together. Around 12.9% of people with fibromyalgia also have IBS, compared to less than 2% of the general population. Looking from the other direction, about 10.7% of hospitalized IBS patients also carry a fibromyalgia diagnosis, versus 1.4% of those without IBS. People with IBS are roughly five times more likely to have fibromyalgia than people without it. This overlap is too large to be coincidental, and it points to shared underlying biology rather than simple bad luck.
The Gut-Brain Connection
Your gut and brain communicate constantly through a two-way signaling network. In fibromyalgia, this communication system appears to malfunction at several points. The central feature of fibromyalgia is a nervous system that amplifies pain signals, a process called central sensitization. That same amplification doesn’t stop at muscles and joints. It extends to the nerves lining your digestive tract, making your gut hypersensitive to normal stretching, gas, and movement of food through the intestines. Sensations that a healthy gut would ignore get flagged as painful or urgent, which can trigger cramping and diarrhea.
The autonomic nervous system, which controls involuntary functions like heart rate and digestion, also shows signs of dysfunction in fibromyalgia. When the branch responsible for “rest and digest” functions misfires, it can speed up or slow down the muscular contractions that push food through your intestines. This intestinal dysmotility helps explain why some people with fibromyalgia swing between diarrhea and constipation, sometimes within the same week.
Serotonin’s Double Role
Most people think of serotonin as a brain chemical tied to mood, but roughly 90% of your body’s serotonin is actually produced in the gut. There, it plays a direct role in controlling how fast your intestines move and how much fluid they secrete. Too much serotonin activity in the gut speeds things up, causing diarrhea. Too little slows things down, leading to constipation.
People with fibromyalgia tend to have lower serotonin levels in their blood overall, and the gut bacteria that help produce serotonin, particularly certain species in the Ruminococcus family, are found in reduced numbers in fibromyalgia patients. This imbalance doesn’t always push things in one predictable direction. Instead, it destabilizes the system, making bowel habits erratic. A gut that can’t properly regulate serotonin signaling is a gut that overreacts to meals, stress, and hormonal shifts.
Gut Bacteria and Bacterial Overgrowth
The community of bacteria living in your intestines plays a surprisingly large role in fibromyalgia symptoms. Research consistently finds that people with fibromyalgia have an altered gut microbiome, with fewer beneficial species and changes in how those bacteria process nutrients and neurotransmitters. These shifts can increase intestinal permeability (sometimes called “leaky gut”), allow low-grade inflammation, and disrupt the chemical signals traveling from gut to brain.
One small but notable study found that 100% of fibromyalgia participants tested positive for small intestinal bacterial overgrowth, or SIBO, a condition where bacteria colonize parts of the small intestine where they don’t belong. When those bacteria ferment carbohydrates before your body can absorb them, the result is gas, bloating, and often diarrhea. That particular finding hasn’t been replicated in larger studies, so the true prevalence of SIBO in fibromyalgia remains uncertain. Still, it highlights how disrupted gut flora can translate directly into digestive symptoms.
Medications That Make It Worse
If you’re being treated for fibromyalgia, the treatment itself may be contributing to your diarrhea. One of the most commonly prescribed medications for fibromyalgia, duloxetine, lists diarrhea as a known side effect. It can occur as a routine side effect during the adjustment period or as a sign of a more serious reaction. Other medications in the same class carry similar risks. If diarrhea started or worsened after beginning a new medication, that timing is worth noting and discussing with your prescriber, since switching to an alternative may resolve the problem entirely.
Dietary Changes That Help
Because the gut plays such a central role, dietary adjustments can make a real difference. The most studied approach is a low-FODMAP diet, which limits certain fermentable carbohydrates found in foods like wheat, onions, garlic, apples, and dairy. These carbohydrates are poorly absorbed in the small intestine and get fermented by gut bacteria, producing gas, bloating, and diarrhea in sensitive individuals.
In a study of fibromyalgia patients who followed a low-FODMAP diet (reducing their daily FODMAP intake from about 25 grams to 2.5 grams), IBS symptom scores dropped by 50%. What surprised researchers was that the benefits extended well beyond the gut. Pain scores improved, and participants reported better daily functioning and overall well-being. The correlation between gut symptom improvement and reduced fibromyalgia impact was statistically significant, reinforcing that calming the gut can calm the whole system.
Adherence in that study averaged 86%, suggesting the diet is manageable for most people once they learn which foods to limit. A low-FODMAP diet is typically done in phases: a strict elimination period of two to six weeks, followed by gradual reintroduction to identify your personal triggers. Lactose and gluten restriction have also been explored in fibromyalgia, though the evidence is stronger for the broader FODMAP approach.
Telling the Difference From Other Causes
Not all diarrhea in someone with fibromyalgia comes from fibromyalgia. Celiac disease, inflammatory bowel disease, thyroid disorders, and infections all cause diarrhea and can coexist with fibromyalgia. Red flags that suggest something else may be going on include blood in the stool, unintentional weight loss, diarrhea that wakes you from sleep, and fever. These warrant separate evaluation rather than being attributed to fibromyalgia by default.
If your diarrhea follows a pattern tied to meals, stress, or specific foods, and comes with bloating and cramping but no alarming symptoms, it’s more likely part of the fibromyalgia-IBS overlap. Keeping a food and symptom diary for two to three weeks can help clarify triggers and give your healthcare provider useful information to work with.