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Quercetin in Lyme disease by Marty Ross MD image.

In chronic Lyme and associated diseases quercetin is an herbal medicine that

  • decreases pain,
  • limits and improves Herxheimer die-off reactions,
  • treats Mast Cell Activation Syndrome, 
  • improves bladder inflammation and irritation in interstitial cystitis, and
  • decreases allergic reactions.

Anti-inflammatory and Antioxidant

Through a variety of mechanisms quercetin lowers inflammatory cytokines and prostaglandins. Cytokines are made by the immune system in response to chronic infections and the killing of Lyme germs. Cytokines treat infections by turning on various white blood cells, but also cause pain, achiness, fatigue, hormonal dysregulation, and poor sleep. In chronic Lyme and associated diseases the immune system makes too many cytokines. In a sense, Lyme disease is a syndrome of cytokine dysregulation and excess. As a I tell my patients, in some ways it is a misnomer to say someone has Lyme disease symptoms. In fact what they really have are excess cytokine symptoms and other symptoms of organ or tissue injury.

A Herxheimer Die-off reaction is the result of a cytokine flare (increased cytokine production by the immune system) in response to antibiotics killing germs. In a Herxheimer die-off reaction, Lyme symptoms worsen significantly when antimicrobials are started or changed.

Pharmaceutical medicine does not have effective anti-cytokine agents that are safe to use in chronic Lyme and associated diseases. Steroids can lower but suppress the immune system making it hard to treat the Lyme infection. Others like Remicaide also suppress the immune system in harmful ways.

Regarding inflammatory prostaglandins, there are pharmaceutical treatments like ibuprofen and aspirin. However these medicines do not lower cytokines. They also injure the lining of the stomach which can lead to stomach pain and even bleeding. I do not recommend medicines like ibuprofen, naprosyn, or aspirin in Lyme disease but prefer to work with quercetin and other herbal anti-inflammatories instead. Based on my observations, quercetin is as effective at lowering pain from prostaglandins, but it does not carry any of the risks and therefore is a better medicine.

Interstitial cystitis is a condition with symptoms similar to bladder infections. Lyme and/or bartonella coinfections cause inflammation of the bladder lining. This leads to increase urination urges, frequency of urination and sometimes burning with urination.

Allergy Medicine and Mast Cells

I also use quercetin to treat my patients who have allergies or Mast Cell Activation Syndrome that worsens their illness. Many people with Lyme disease have food or environmental allergies that hurt their health. Quercetin limits allergies in two ways. First it stablizes immune system cells that make and release histamines. With quercetin certain immune system cells do not release histamines when they are provoked by environmental allergens like plant pollens and dust mites or by foods. Quercetin also decreases inflammation in allergies by decreasing leukotriene inflammation chemicals made in allergies. For more information read Mast Cell Activation Syndrome & Lyme.

Method of Action for Pain, Herxheimer Die-Off Reaction, and Interstitial Cystitis

Quercetin is a strong anti-inflammatory. First it limits the expression of NF-kB which is a signalling chemical inside cells that causes genetically derived messengers for inflammatory chemicals production. As a kinase enzyme inhibitor, quercetin also decreases the production of inflammatory cytokines inside of cells. It is also a strong antioxidant that deceases oxidizing agents that trigger inflammation. Finally, it blocks cyclooxygenase enzymes used to produce inflammatory prostaglandins.


Quercetin is a bioflavanoid that comes from a variety of foods like red onions, grapes, apples, berries, cherries, broccoli, citrus fruits, green tea and capers.

I recommend using a quercetin product designed to increase absorption. Some modify the quercetin molecule as quercetin chalone to increase water solubility and absorption.


  • For pain, Herxheimer die-off reactions, and interstitial cystitis, I recommend Quercetin 250mg, 2 pills 3 times a day.
  • For allergies I recommend Quercetin 250mg 2 pills 2 times a day.


Quercetin is very safe to take. In theory it may alter the effectiveness of quinolone antibiotics like Levaquin, Cipro, and Avelox. However, in practice I do not see this to be the case.


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