One family came to me after their 11-year-old daughter had been struggling with stomach aches, poor appetite, and nausea for months. She was missing school, and every GI test came back normal. The family had tried changing her diet, adding probiotics, and even therapy because they were told it might just be stress.

But when we took a closer look, we noticed something bigger. In addition to her gut symptoms, she was unusually tired, had trouble focusing, and had recently developed pain in her knees. Her symptoms fit a pattern I’ve seen before — especially in children with Lyme disease.

Once we started treatment for Lyme and a co-infection, her stomach issues improved, and she started returning to school with energy and confidence.

Gut symptoms in Lyme disease are incredibly common, yet they’re often misunderstood, dismissed, or treated in isolation. But for many people, the gut is one of the first systems affected by Lyme disease or a co-infection. And when we pay attention to those clues, we often catch the illness sooner and treat it more effectively.

How Lyme Disease Triggers Gut Symptoms

Lyme disease doesn’t just affect joints or the brain. It can also interfere with how the body manages digestion.

That’s partly because the autonomic nervous system, which controls things like gut motility and blood flow after meals, can be disrupted by infection. When those signals get out of balance, individuals can experience nausea, bloating, feeling full after just a few bites, or even fatigue after eating. In some people, these changes show up before the more familiar signs of Lyme disease appear.

In fact, a study of 314 patients with early Lyme disease found that 23% experienced anorexia, 17% reported nausea, and 10% had vomiting — clear evidence that the gut is often involved from the very beginning.¹

The immune system also plays a role. Inflammation triggered by Lyme disease or a co-infection may affect digestion, increase gut sensitivity, or alter how the body handles food.

Testing Pitfalls: Why Normal Results Don’t Always Mean You’re Fine

Many of my patients undergo GI workups — endoscopy, colonoscopy, abdominal imaging — with normal results. But normal tests don’t mean normal function. Lyme disease and its co-infections often disrupt motility and nervous system signaling in ways standard testing can’t detect.

7 Gut Clues Lyme Disease Might Be Involved

If you have any of these symptoms and other signs of a tick-borne illness — like fatigue, brain fog, or joint pain — your gut issues may be due to Lyme disease or a co-infection.

1. Persistent nausea with normal labs and imaging

2. Early satiety — feeling full after just a few bites

3. Bloating that isn’t explained by diet or IBS

4. Constipation alternating with diarrhea

5. Heartburn or reflux that doesn’t improve with medications

6. Abdominal cramping or pain despite normal GI testing

7. Fatigue or dizziness after eating, especially in patients with POTS

Special Note on Pediatric Cases

In children, Lyme-related gut symptoms can look like refusing to eat or having stomach aches at school. Sometimes they’re mistaken for anxiety. But these signs should be taken seriously — especially if they come with behavior changes, fatigue, or joint pain.

Gut Symptoms Can Mimic Other Conditions

Gut symptoms in Lyme disease can mimic:

1. Functional Dyspepsia

2. Irritable Bowel Syndrome (IBS)

3. Gastroparesis

4. Mast Cell Activation Syndrome (MCAS)

5. Small Intestinal Bacterial Overgrowth (SIBO)

If you’ve been told you have one of these conditions but treatments haven’t helped, it may be time to consider Lyme disease or a co-infection.

Why Gut Symptoms Deserve More Than a GI Referral

Too often, patients are sent to a GI specialist and given a diagnosis of IBS, functional dyspepsia, or reflux without a broader evaluation. In the context of Lyme disease, those labels don’t always help and they certainly don’t explain why digestion has changed.

If we ignore gut symptoms in Lyme disease, we may miss early neurologic or autonomic signs of the infection and delay effective care.

How I Treat Gut Symptoms in Lyme Disease

Every patient is different, but addressing gut symptoms is often a key part of treatment. My approach includes:

1. Modifying antibiotics if GI symptoms worsen

2. Adding probiotics strategically, spaced from antimicrobial doses

3. Evaluating co-infections like Babesia and Bartonella that affect digestion

4. Supporting autonomic regulation with hydration, salt, pacing, and sometimes medication

5. Managing nausea, bloating, or GI motility issues with symptom-specific therapies

6. Addressing gut symptoms as part of the Lyme picture, not in isolation

Final Thoughts

When your gut is telling you something’s wrong, it’s not just a digestive issue—it may be an early sign of a complex systemic illness.

Gut symptoms in Lyme disease deserve serious attention. They may be one of the most important clues we have.

Resources

1. Signs and Symptoms of Untreated Lyme Disease
2. Dysautonomia
3. Stomach pain can be a symptom of Lyme disease
4. Could Lyme Disease Be Wrecking Your Gut Without You Knowing It?
5. Lyme Science Blog