How Oxalates Affect Your Gut, Urinary Tract, and Risk of Autoimmune Conditions

In personalized lifestyle medicine, sometimes one person’s superfood is another person’s poison. Such is the case with oxalates, which are found in high concentrations in many presumed health foods. Once I started testing, I realized that many of my patients were experiencing the downstream consequences of excess oxalate intake, usually in the form of green smoothies full of spinach, kale, and other greens.

Oxalates are naturally occurring compounds in foods like spinach, kale, nuts, beans, and even chocolate that can interfere with the absorption of vitamins, minerals, and other nutrients. In susceptible individuals, foods that seem healthy can become toxic. They are considered “anti-nutrients” because they protect the plant against predators, from harmful bacteria to insects and animals. In additional to oxalates that originate in food, called exogenous oxalates, the human body also produces them mainly in the liver from excess vitamin C, fructose, and yeast. (Other anti-nutrients include phytic acid and lectins). Unfortunately, oxalates form painful crystals in various places such as the kidneys, bladder, vulva, gut wall, and other mucosal membranes in susceptible people.[1]

What Increases Your Risk of Oxalate Overload?

You have to be sensitive to them, because of your genetics, gut bacteria (dysbiosis, or missing the microbes that process them), or nutritional deficiencies, like vitamin B6, magnesium, and thiamine.[2] The gene involved in oxalate breakdown is called SLC26A1. The bacteria that break down oxalates are the Oxalobacter formigenes and Lactobacillus species. Eating too many oxalates, like more than 250 mg a day, also puts you at risk for problems.

Personally, I have dirty oxalate genes, meaning that I don’t break down oxalates in food. Additionally, I am missing the bacteria that break them down in my gut, so I have a double hit – and as a result, oxalates are very high in on my urinary organic acid tests.

There’s no specific estimate on how many people suffer from this, but I’ve noticed this in a large portion of the women I work with. You can get diagnosed in a simple urine test that measures oxalates, called the organic acid test. For best results, work with a functional medicine clinician. You can also test for the oxalate-degrading bacteria in your stool.

What Symptoms Are Caused by Oxalate Overload?

  • Gut problems including bloating (oxalates can irritate the mucosal lining throughout the body)
  • Chronic pain
  • Kidney stones
  • Interstitial cystitis (a syndrome of painful bladder)
  • Vulvar pain and vulvodynia
  • Joint pain
  • Inflammation (muscle stiffness, bloating)
  • Autoimmune conditions
  • Mineral deficiency
  • Autism

How Can Oxalate Overload Be Prevented or Treated? 

The best way to prevent or treat oxalate overload is to reduce the consumption of high oxalate food. It’s best to switch first to a moderate oxalate diet (if you go too low on oxalates too fast, you can form painful crystals). Then after 2-4 weeks, try low oxalate. Probiotics and oxalate-degrading supplements may help too. Aim for a healthy calcium-oxalate ratio in the body. A reasonable goal is to consume less than 100 mg of oxalate per day.

Additionally, increase calcium intake normal to high (800-1200 mg/day for adults) to reduce the urinary excretion of oxalate (Note that a diet high in oxalates > 250 mg/day and/or a diet low in calcium increase urinary oxalate excretion.) Limiting protein intake can also reduce the urinary excretion of oxalates. Finally, the intake of pyridoxine (vitamin B6) reduces the excretion of oxalate.[3]

Summary: What Helps?

  • Eat low-to-medium oxalate foods: Wild-caught fish, pastured poultry, grass-fed beef, bananas, Golden Delicious apples, cabbage, bok choy, broccoli, Brussel sprouts, celery, endive, cauliflower, cucumber, zucchini, lettuce, onions, and mushrooms.
  • Avoid the high oxalate foods, which tend to be the dark leafy greens. One cup of raw spinach contains around 656 mg oxalate. This is a great resource listing oxalate count in various foods.
  • Supplement with vitamin B6, calcium, and magnesium, which can reduce the effect of oxalates.
  • Skip black tea and instant coffee, both very high in oxalates. I used to drink instant Starbucks decaf coffee all day long and learned it was a significant source of my oxalate overload. Green and herbal tea are lower in oxalates.[4]
  • Probiotics can help. Oxalobacter formigenes and Lactobacillus species as mentioned previously help to degrade oxalates in the gut. Taking these as probiotics may help but I’m not aware of data showing a benefit at this time.

It may seem restrictive, but after one week on a low oxalate diet, I lost all of my abdominal bloating and dropped a few pounds. I felt better within one day, and that makes the lifestyle change easier. If I could do it, you could too!

Here’s one of my go-to low-oxalate lunches….

Dr. Sara’s Low Oxalate Bowl

Base of 1 cup of kelp, shirataki noodles or shredded cabbage
Cauliflower, chopped
Zucchini, chopped
Mushrooms, chopped
Cucumbers, chopped
Cilantro, chopped
top with fresh wild salmon

Your turn. Have you noticed problems with oxalates? Have you performed organic acid testing on yourself or your patients/clients and see issues with oxalate metabolism? Have you tried a low-to-moderate oxalate diet, and if so, what did you notice?


[1]Peck, A. B., et al. “Oxalate-degrading microorganisms or oxalate-degrading enzymes: Which is the future therapy for enzymatic dissolution of calcium-oxalate uroliths in recurrent stone disease?.” Urolithiasis 44, no. 1 (2016): 45-50.

[2] Mehta, M., et al. “The role of the microbiome in kidney stone formation.” International Journal of Surgery 36 (2016): 607-612; Sadaf, H., et al. “Role of gut microbiota against calcium oxalate.” Microbial Pathogenesis 109 (2017): 287-291.

[3] Prezioso, D., et al. “Dietary treatment of urinary risk factors for renal stone formation: A review of CLU working group.” Archivio Italiano di Urologia Andrologia 87, no. 2 (2015): 105-120.

[4] Charrier, M. J., et al. “Oxalate content and calcium binding capacity of tea and herbal teas.” Asia Pacific Journal of Clinical Nutrition 11, no. 4 (2002): 298-301.