A Case That Surprised Both Patient and Clinician

One of my patients recently developed black teeth after taking antibiotics for Lyme disease. The discoloration appeared suddenly and was deeply alarming to her — dark streaks and patches that looked like severe decay or even necrosis. She feared something irreversible had happened.

But when she visited her dentist, everything changed. The “blackness” polished off completely. The enamel underneath was healthy. What looked like a dental emergency turned out to be extrinsic staining, not tooth death or permanent damage.

This case highlights something important: in Lyme disease, dramatic changes in the appearance of your teeth — especially in the middle of treatment — can have simple, reversible explanations. Antibiotics, dry mouth, nerve involvement, and autonomic dysfunction can all contribute to staining that looks far worse than it truly is.

Why Do Teeth Turn Black After Using Antibiotics?

Medication-Related Staining

Many antibiotics used in Lyme treatment can bind to plaque or small irregularities on the enamel surface. Doxycycline, amoxicillin–clavulanate, metronidazole, and even common agents like Pepto-Bismol can all leave dark surface pigments. Herbal tinctures and chlorhexidine rinses can do the same. Once the surface is polished, the dark coating lifts away.

Dry Mouth From Autonomic Dysfunction

Lyme and co-infections frequently cause autonomic instability, which reduces saliva production. When saliva drops, the mouth becomes more acidic, plaque builds more quickly, and pigment-producing bacteria flourish. This environment makes any staining — whether from medications or bacteria — far more visible.

Neuropathy and Brushing Patterns

Neurological symptoms in post-treatment Lyme disease, including numbness, tingling, and changes in oral sensation, can subtly affect how patients brush. When brushing pressure or consistency decreases, plaque accumulates in areas that are harder to reach or feel, allowing dark pigments to settle into those spots.

Shifts in the Oral Microbiome

Antibiotics don’t only affect Lyme bacteria, they also change the balance of organisms in the mouth. Certain chromogenic (pigment-producing) bacteria can become more prominent during treatment. These organisms are well-recognized in dentistry for creating brown or black surface stains along the gum line or between teeth. As the oral flora stabilizes and plaque is removed, these stains typically resolve.

Effects of Co-Infections

Co-infections such as Bartonella and Babesia may contribute to gum inflammation, enamel sensitivity, and vascular irritation. While they do not directly “cause” black stains, they can make the oral environment more reactive and allow staining to appear more pronounced.

True Tooth Necrosis

On rare occasions, a tooth may appear dark from the inside rather than on the surface. Internal gray, purple, or black discoloration usually indicates pulp injury, trauma, or loss of blood flow to the tooth. Unlike surface staining, internal necrosis does not polish off and requires dental evaluation.

Clinical Takeaway

My patient’s experience is a reminder that developing black teeth after antibiotic treatment can be caused by external pigments, not decay or permanent enamel loss. Autonomic dysfunction, dry mouth, neuropathy, and microbiome shifts can all make staining more likely or more noticeable.

True tooth necrosis is uncommon but should be ruled out if the discoloration appears internal or does not improve with cleaning.

In most cases, however, the darkening is temporary, reversible, and far less dangerous than it appears. A simple dental cleaning often reveals a healthy tooth beneath the alarming color.

Have you noticed tooth discoloration during Lyme treatment?

Share your story below—your experience may help someone who’s worried they’re the only one.

Resources

1. Frontiers in Neurology. (2024) Dysautonomia following Lyme disease: a key component of post-treatment Lyme disease syndrome? 
2. BMC Oral Health. (2025) Chromogenic bacterial staining of teeth: a scoping review.
3. Dr. Daniel Cameron: Lyme Science Blog. Dental surgery triggers full body pain in patient with severe post-treatment Lyme disease syndrome
4. Dr. Daniel Cameron: Lyme Science Blog. Sjögren’s syndrome secondary to Lyme disease