The Hard Truth About Kidney Stones Part 1 - Stone Formation
Part 1 - Stone Formation
I wish this were simple. Kidney stone formation is nuanced, complicated, non-linear, and still not fully understood. We tend to approach problems with binary thinking: all-or-none, zero-or-one, yes-or-no, black-or-white. That works well for troubleshooting a refrigerator, the car, or computer, but the human body is not binary code. Applying that logic to complex physiology oversimplifies problems, and kidney stone formation is a perfect example.
Kidney stone pathology (nephrolithiasis) is multifactorial. There are many types of kidney stones. Calcium oxalate, calcium phosphate, uric acid, and struvite make up the majority, with calcium-containing stones accounting for most cases. In this article, we will concentrate on calcium oxalate stones.
Human urine consists of about 95% water. The other 5% is “dissolved solutes” or other stuff which varies greatly depending on hydration, nutrition, metabolism, and genetics. Calcium and oxalate are normally excreted in urine. So why do these substances form stones in some people and not for others?
It depends on a concert of interacting factors.
Protective compounds such as citrate and magnesium in the urine make significant difference, as do urinary pH, urine volume, and the concentrations of the stone-forming compounds themselves. Stone formation is ultimately a balance between substances that encourage crystallization and the mechanisms that inhibit it.
Drink Water!
Let’s get this out of the way: You HAVE to drink water!
We typically estimate to drink half your body weight in ounces of water daily. For a 150 pound person, that’s 75 oz of water, roughly 2.3 liters or quarts. For people prone to kidney stones, they need to produce enough urine to keep stone-forming compounds diluted. A general goal is to produce at least 2–2.5 liters of urine per day, which can be achieved by drinking 2.5-3 liters of non-caffeinated, non-carbonated fluid per day.
Requirements for water intake vary with body size, activity, climate, sweating, diet, and medications. Someone working outdoors in a Texas summer requires considerably more water than someone sitting inside an air-conditioned office.
Lower urine volume concentrates calcium, oxalate, uric acid, and stone-forming compounds, increasing stone formation. Higher urine volume dilutes them. This helps explain why kidney stones occur more frequently during hotter months. More fluid is lost through perspiration, leaving less water available for urine production. Hydration is foundational. Any treatment you are attempting to resolve a stone will be futile if you don’t drink enough water.
Genetics Loads the Gun, Environment Pulls the Trigger
Beyond water intake, metabolic and genetic abnormalities are associated with kidney stones. Some people excrete excessive calcium, others produce more oxalate. Some excrete inadequate citrate. Variations in renal handling of minerals makes one person more susceptible to stones than another eating essentially the same diet. In other words, some people are “stone-formers.”
But genetic susceptibility is not destiny. Genes provide the physiological path upon which hydration, diet, gastrointestinal health, microbiome, medications, hormones, and lifestyle operate. For someone with a genetic tendency toward stones, those environmental factors matter even more.
It’s NOT Just a Kidney Problem
One mistake we make with kidney stones is assuming the problem is entirely a kidney problem. Calcium and oxalate have already traveled quite a journey before they ever appear in the urine. Several organ systems influence how much calcium and oxalate ultimately reach the kidneys.
1. The digestive tract
Food enters the gastrointestinal tract, where calcium, oxalate, fat, minerals, and other nutrients are mixed and absorbed. Some dietary oxalate is absorbed through the intestinal wall and enters the bloodstream. Calcium is also absorbed in the intestine, a process strongly influenced by vitamin D. What happens in the gut significantly affects how much calcium and oxalate reach the urine.
2. The liver
Not all oxalate comes from food. The liver also produces oxalate as an end product of normal metabolism. In some people, endogenous oxalate production contributes substantially to the amount of oxalate the kidneys must filter and excrete. Vitamin C can be broken down into oxalate and excreted by the kidneys. This is why high-dose vitamin C supplementation (over 2,000 mg per day) can increase urinary oxalate in susceptible individuals. Food-based vitamin C generally isn't the concern. In addition, we will discuss how lack of B6 contributes to the over-oxalate production in the liver.
3. The parathyroid glands and bones
The four small parathyroid glands, located embedded behind the thyroid are regulators of calcium balance. Through parathyroid hormone (PTH), they coordinate calcium movement from the bones, gastrointestinal tract, kidneys, and bloodstream.
The stone may be found in the kidney, but the physiology behind it involves so many other places in the body. That is why simply telling every calcium oxalate stone-former to “stop eating oxalate, vitamin C, or calcium” misses much of the picture.
To Eat Oxalates or Not Eat Oxalates?
The infamous spinach, sweet potatoes, beets, Swiss chard, rhubarb, almonds, and peanuts are foods often eliminated during kidney stones management. While this recommendation can be useful for acute protocols, we must take a look at the overall picture.
The gastrointestinal tract is an under-appreciated player in kidney stone disease. Calcium normally binds to dietary oxalate within the intestinal tract. This binding takes both the oxalate and calcium out of solution. But fat malabsorption can dramatically change calcium binding, which heavily depends on bile production and gallbladder health.
Remember, bile is necessary for fat absorption. When poorly absorbed fatty acids enter the intestine, they bind calcium. Less calcium is available to bind oxalate. Unbound oxalate is absorbed through the intestinal wall, enters circulation, and eventually is excreted by the kidney. This process is called enteric hyperoxaluria and explains why calcium oxalate stones can occur more frequently in people with inflammatory bowel disease, chronic diarrhea, fat malabsorption, pancreatic insufficiency, or after certain bariatric surgeries.
But remember, oxalate does not come exclusively from food; the liver produces it through the breakdown of collages, called glyoxylate. Normally, the liver diverts glyoxylate away from oxalate by converting it to glycine through a vitamin B6-dependent pathway. When this pathway is overwhelmed more glyoxylate converts to oxalate. This is an important reminder that high urinary oxalate is not just a “too much spinach” problem, it may reflect a combination of intestinal absorption and too much of the liver's oxalate production.
To Eat Calcium or Not to Eat Calcium?
This one surprises people. If you make calcium oxalate stones, it seems logical that eating less calcium should help. In many cases, the opposite is true.
Calcium in food binds oxalate inside the intestinal tract. The resulting calcium-oxalate complex then leaves the body through the stool instead of allowing that oxalate to be absorbed into the bloodstream and into the urine. When dietary calcium is excessively restricted, more free oxalate remains available for intestinal absorption.
For most calcium oxalate stones, adequate calcium from food is preferable to restricting calcium. Timing matters! Calcium consumed with an oxalate-containing meal is positioned to bind that oxalate in the GI tract, keeping free oxalates and free calcium in the urine.
The question shouldn't simply be, “How much calcium are you eating?” It should be, “Where is the calcium coming from and where is it going?” Many “stone formers” have an ironic osteopenia or osteoporosis and elevated calcium urinary excretion. This implies a calcium regulation issue and potentially parathyroid dysregulation.
Don't Forget the Parathyroid
One important condition to rule out is primary hyperparathyroidism. The parathyroid glands, the governors of calcium balance, use your bones as your calcium savings account. When calcium levels in the blood fall, the parathyroid glands release parathyroid hormone (PTH) to restore that level.
You see, your blood calcium level is VERY tightly regulated because calcium is essential for many critical functions, including nerve signaling, muscle contraction, heart function, and blood clotting. Your body works hard to keep calcium in the bloodstream within a narrow range, even if that means pulling calcium out of your bones to do it. This is why a normal serum calcium level does not tell us what is happening with calcium balance throughout the body. Your blood calcium will look perfectly fine while calcium is being lost from the skeleton or excessively excreted through the kidneys.
PTH increases calcium reabsorption by the kidneys, stimulates activation of vitamin D to increase intestinal calcium absorption, and then increases bone resorption, releasing stored calcium from the skeleton into the bloodstream. Talk about a non-linear concept! To recap - parathyroid tells the kidney to hold onto calcium, it increases calcium absorption from your GI, and then increases bone turnover to dump calcium - all attempts to tightly balance calcium in your blood.
In primary hyperparathyroidism, PTH secretion is abnormally elevated. This increases calcium release from bone and elevates blood calcium (hypercalcemia) and in urine (hypercalciuria). When more calcium is delivered into the urine, that excess calcium combines with oxalate or phosphate, making kidney stones.
This is why recurrent calcium stones, particularly when accompanied by elevated or high-normal serum calcium, warrant evaluation of serum calcium, albumin, PTH, vitamin D, kidney function, and 24-hour urinary calcium. Sometimes a kidney stone is the first clue that a much larger problem with calcium regulation exists.
As always, understanding the systems and circumstances that contribute to stone formation gives you clues on how to fix things. Hydration matters, eating calcium WITH oxalate containing foods helps, and working up the parathyroid, liver, and digestive health adds to the understanding. In Part 2 - we will go into strategies for eliminating kidney stones and maintaining kidney health to prevent stone formation.

