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Undoctored Protocols: Calcium Oxalate Kidney Stones

kidney stones Passing a kidney stone is often described as one of the few pains worse than childbirth. Over 7 years, half of all people who have had a kidney stone will experience a recurrence, greater risk over a longer period. The majority of kidney stones are made from calcium oxalate, so our Undoctored efforts focus on reducing the urinary concentrations of both calcium and oxalate to inhibit crystallization into stones.


Urine saturated with calcium and oxalate allows crystals to form and, over time, grow to become “stones” that block urine if passed into the ureters (leading to the bladder), leading to bleeding in the urine and excruciating pain. A key strategy is therefore to keep urine dilute and prevent calcium and oxalate from crystallizing, partially achieved by hydrating well. This is exceptionally important.

Gauging the adequacy of hydration, however, is imprecise. Rules such as “drink half your weight in water per day,” do not factor in level of physical effort, time of year/ambient temperature, clothing, variation in sweating, or individual urine concentrating ability and are therefore potentially misleading and should not be generally used. A better, though crude, method is to observe urine color and hydrate to keep it from becoming amber, maintaining a light yellow tint at all times. Another way is to dip your urine with dipsticks (widely available in pharmacies), never allowing urine specific gravity to go higher than 1.010. Several manufacturers are developing portable devices that measure sodium concentration of sweat, an indirect gauge of hydration status. Stay tuned for discussions about these devices as they become available.

Rebuild Bowel Flora

Supplement with a high-potency, multi-species probiotic, as in the Undoctored Wild, Naked, and Unwashed program. Check your preparation to make sure it contains at least one, preferably several, of the following species: Bifidobacteria infantis, Bifidobacteria lactis, Bifidobacteria breve, Bifidobacteria longum, Lactobacillus paracasei, Lactobacillus acidophilus, Lactobacillus plantarum, Lactobacillus or Lactobacillus gasseri, species that reduce urine levels of oxalate. Garden of Life Raw products and Renew Life Ultimate Flora Extra Care are two excellent choices. In future, there will likely be probiotics that include Oxalobacter formigenes that further reduce urinary oxalate levels. It is not yet clear how long a probiotic must be taken for full benefit, or on what schedule (e.g., 4 weeks every 6 months?), particularly when combined with a prebiotic fiber program, as in Undoctored. For full assurance of benefit, taking the probiotic chronically or on a repetitive schedule assures continual reseeding of bowel flora; we shall update this unanswered question as new data emerges.

Magnesium Citrate

This form of magnesium, while not as well absorbed as our preferred forms, is best at blocking calcium oxalate crystal formation. Ideally, 400 mg three times per day. Both magnesium and citrate (citric acid) block the formation of calcium oxalate crystals. Magnesium citrate is therefore a convenient means of obtaining both.

Vitamin B6

Taken as the most active form, pyridoxal 5’-phosphate (rather than the less well metabolized pyridoxine), 50 mg per day, vitamin B6 also blocks calcium and oxalate from crystallizing in urine.


Abratt VR, Reid SJ. Oxalate-degrading bacteria of the human gut as probiotics in the management of kidney stone disease. Adv Appl Microbiol. 2010;72:63-87.

Oppici E, Fargue S, Reid ES et al. Pyridoxamine and pyridoxal are more effective than pyridoxine in rescuing folding-defective variants of human alanine:glyoxylate aminotransferase causing primary hyperoxaluria type I. Hum Mol Genet. 2015 Oct 1;24(19):5500-11.

Reddy SV, Shaik AB, Bokkisam S. Effect of potassium magnesium citrate and vitamin B-6 prophylaxis for recurrent and multiple calcium oxalate and phosphate urolithiasis. Korean J Urol. 2014 Jun;55(6):411-6.

Go to Forum discussion.


Let's discuss the Undoctored Protocol for Calcium Oxalate Kidney Stones. It's important to stress that the basic Undoctored Wild-Naked-Unwashed program still matters. These protocol strategies are in addition to the basic strategy.


Start with hydration. It helps to think of calcium oxalate kidney stones as something like making rock candy as a kid. Remember how you did that? You concentrated sugar in solution by heating it, and then you allowed it to cool with a piece of string hanging in it. As it cooled, it crystallized, into rock candy (into crystal). The same principle applies to calcium oxalate kidney stones. If you allow urine to be concentrated, then calcium and oxalate is going to crystallize, and develop stones over time.

Your best protection against that is stay well hydrated. How do you do that? You can follow those rules, like “drink half your weight in ounces”, but you know what, that doesn't factor in genetics, kidney concentrating ability (urine concentrating ability), ambient temperature — there's so many factors that affect how much water you need, that those rules are not really all that helpful. They're a starting place, but that's about it.

Looking at your urine color, helps. When you urinate, it should be a light yellow or clear, but not that amber, darkish color. If it's dark, you know you're not hydrating properly. Of course, when it's hot out, or you're sweating a lot, you need to compensate for that, with greater hydration. You could go to the pharmacy, and buy dipsticks for specific gravity — cheap and easy — and you try to keep your specific gravity below 1.010.

We will have soon, devices that help us measure sweat sodium, as an index of hydration. We may even have a smart phone device. It plugs into your phone; apply it to your skin, and it gives you a read-out. When those devices come out and are available, we'll talk about it in the Undoctored program. Right now we don't have access to those things.

Bowel flora

Just as in the basic program, is very important. But stayed tuned, because there may be some new preparations on the market that include the Oxalobacter species that reduces urinary oxalates even further. There is no commercial preparation yet with that species, but they may become available. It's also unclear how long you should continue a probiotic. It's probable that you have to cycle through probiotics every few months.

In other words, perhaps 6 weeks, 8 weeks of a high potency multi-species probiotic — maybe do that every 3 months, every 6 months — no one really knows. You're trying to ensure that the species that reduce urinary oxalate persist and continue. So stay tuned to that conversation, as we have better data on exactly how to manage that schedule. In the meantime, I would at least do the starting program of 6 to 8 weeks of a multi-species high potency probiotic, and consider repeating that every few months.

Mg citrate: 400 mg 3 times per day

Consider replacing your magnesium supplement with magnesium citrate, instead of the malate, or bicarbonate, or other forms. Magnesium inhibits formation of calcium oxalate stones, as does citrate (citric acid). Magnesium citrate is the preferred form when you have kidney stones. A useful dose is 400 milligrams 3 times a day. It's a little hard to remember, but 3 times a day is best.


Some people benefit by taking vitamin B6 as the Pyridoxal 5-prime phosphate. See the Undoctored book for more detail on that; also on the Undoctored Inner Circle website below [below the video on the Protocol page].

So those are the additional strategies that stack the odds in favor of not having any recurrence of your calcium oxalate kidney stones. It takes on-going efforts. You have to stick to it. Hydration, for instance, is a constant effort.

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