CoeTie4Hard unwanted objects made in the kidneys, stones can cause pain, bleeding, and urinary tract obstruction. Because stone surgery often infects the urinary system, and bacteria easily infect stones retained in the kidneys, infection follow stones like a shadow.

Stones surprise patients by their smallness, for all the trouble they cause, or by their largeness to think they passed through the urinary tract.

But small or large, many or few, stones provoke little love. Most who form them desire no more. Yet, left to themselves, stones recur. Over half of first time stone formers form another stone within 5 – 10 years. Once recurrent, stones form – on average – every 2 – 4  years.

So stone patients must pursue prevention and not imagine their disease will stop of itself.

Prevention consists in the search for causes and the administration of treatment. This site exists to guide both.

Crystals Make Stones Hard

Urine proteins molecules stick to tiny crystals and to each other as if designed to dispose of unwanted things. One can see in many morning urines tiny harmless crystal aggregates passed unknowingly and without harm.

In those predisposed, such protein crystal composites grow so large and numerous they can produce brief attacks of pain and bleeding but, being still too small to see on radiographs, escape detection. Such ‘crystal attacks’ are common in children with genetic hypercalciuria. Uric acid crystals can make a visible orange sludge or gravel.

When protein crystal composites grow grow big enough to obstruct the urinary tract and cause pain and we call them stones.

Very rarely urine organic molecules themselves make ‘soft’ stones that cause mild pain on passing.

Perhaps the true cause of stones hides in the chemistry of urine organic molecules, but for the moment these molecules are irrelevant to patients and their physicians. We do not know which ones most matter and about what is wrong with them that they permit stones we know essentially nothing.

So to prevent stones we work to prevent crystals. We search for causes of crystal formation, and act against them.

Stones are Crystal Artefacts

In human urine, calcium frequently crystallizes with oxalate and phosphate to produce the common calcium oxalate or calcium phosphate stones.

Other less common crystals form their own stones: Uric acid, a byproduct of nucleic acid metabolism; cystine, an amino acid that the genetic kidney tubule disease called cystinuria may liberate into urine in great excess; struvite, a crystal created by bacteria breakdown of urea, a normal urine constituent. Many drugs form crystals.

Because crystals can form independent of one another, many stones contain mixtures of them.

Like volcanic lava, an insect caught in amber, or the vague fossil tracings of some long lost species traced out in an otherwise indifferent rock, the crystals of a stone tell about a particular person with shocking precision and undeniable truth.

To find calcium oxalate crystals means such crystals were indeed once formed by that patient, and the same for all other crystals. Each crystal is a proof of past formation.

But unlike artefacts of a vanished age the proof in stones matters immediately, for in the person who made the stone those very same causes that once made its crystals may well yet operate and pose risk for more.

You might think such artefacts would attract the most intense interest and study. But no; stones are often discarded.

Stones Inform and Guide Prevention

Being as they are the artifacts and physical proof of past crystal formation, the crystals in stones guide all treatment. We can prevent stones only by preventing crystals. In any one patients the stones tell us what crystals we need to prevent. Otherwise than attend to the evidence written in stones we act in ignorance.

Stones are analysed by special laboratories

Specialized laboratories analyse stones at a moderate price.

One company has posted its prices. If you send the stone and pre-pay it is $40.00 with 2 photographs of the stone. Your doctor can get it for $35.00. This is only one of many companies that sell the service.

The report from any stone analysis laboratory is usually a single page that lists each type of crystal found in the stone and a rough approximation of the percentage of the stone each crystal accounts for.

The stones are powdered for the analysis. So a batch of stones will be cheap per stone but powdering of the batch will mix everything together; you get only an average. I would batch stones passed at one time. Analyse individually stones passed at different times because things change.

General measures can help prevent recurrence in people who have formed only one calcium stone

Although people believe that high fluid intake will reduce stone formation, a detailed review of the literature found only one reliable trial to support that belief.

This figure from that one trial shows that formation of a new stone was delayed by high water intake in patients who had formed a single stone. After just one stone nearly 30% of people who did not increase their urine volume (Group 2, average 1 liter daily) had formed at least one more by 5 years whereas only 10% of those with a higher fluid intake (Group 2, 2.6 liters daily) did so.

As expected urine supersaturation fell with higher volume – 2.6 vs. 9.9 and 0.48 vs. 1.58, treated vs. controls, CaOx and CaP SS respectively. A fall of supersaturation would reduce the free energy of crystal formation and that could explain the fall in new stone formation.

But it is hard to do everything with just fluids. The day is long and various. We sleep by night. People forget. Crystals never sleep. Crystals never forget. In a trial, with prompting from nurses, people will maintain a high urine flow, but how about the usual situation? You want fluids. But you also want whatever treatment aims most precisely at the crystals you form. That means you need to know what those crystals are. And to find out what the crystals are the stones must be analysed.

Crystal specific treatment is far better than general measures for patients with more than one calcium stone

The patients in the water trial had formed only one stone each, so far as could be told, and only 25% of those who did not raise their urine volumes (Group 2) had another stone in five years. Among people who have formed at least several stones, 60% in the control groups of trials that tested specific treatments formed at least one more stone within 3 years. By contrast only 15 – 20% of those receiving specific treatments formed another stone during the same interval. These control patients all raised their urine volumes. None had average volumes so low as the 1 liter/day in the control group for this trial.

High water intake may well be ideal for those who have formed only one stone, but the large numbers of patients who have formed more than one stone will predictably form more stones at much higher rates and benefit greatly from treatments that focus on their specific stone crystal.

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44 Responses to “WHAT KIDNEY STONES ARE”

  1. MH Taylor

    You note that “Very rarely urine organic molecules themselves make ‘soft’ stones that cause mild pain on passing.” My 23 year old daughter has episodic kidney pain. When the pain gets worse, she will pass debris in her urine–that sometimes looks like sand, or sometimes consists of larger matter. This can be quite painful. Two times her stones have been sent away for analysis; both times the result was “100% organic matter–blood and tissue.” One stone was measured within each sample and they were: 4.0mm x 6.0mm x1.00 mm weight 1.0 mg, and 1.5mm x 2.0mm x 1.5mm weight 17mg. Her urologist was very dismissive that she could be in pain and said he could not help her, as he found no structural reasons for her pain. Her nephrologist is sympathetic but doesn’t suggest any treatment plan. What could be causing these painful stone-like debris of organic matter, and what additional tests or other avenues should her doctor consider?

    • Fredric L Coe, MD

      Hi MH, Protein stones can be painful, passing blood clots down a ureter is not without pain, too. Almost certainly, given her age, these protein aggregates are being formed around crystals. I would advise sending the samples to Litholink where stone analysis is very refined (I founded Litholink but have no financial interests in it. There will be crystals, and these can be prevented. Regards, Fred Coe

  2. Sarah

    Hi Dr Coe! I have to say I nerded out with your paragraph “You might think such artefacts would attract the most intense interest and study. But no; stones are often discarded.”

    I agree! I think they are so fascinating! Some downright beautiful! I had a whole collection saved but sadly a doctor wanted it and My whole collection, that I was only proud of, was wiped out. It’s ok… I’m rebuilding! I believe I get uric acid stones. Anyway I passed one today, not even terribly big, but it took 3-4 days. I was looking at it under one of my kids microscopes (awful quality but enough to assist in satisfying my curiosity). I’m pretty shocked at what I saw with only 10-20x magnification. I saw the normal crystalline formations but also what look like (and I apologize because it’s kinda gross) roots or insect legs. Like other organic matter under a microscope it had translucent qualities with bits inside the root/leg structures. I thought to look up if maybe parasites or something could pass as part of a stone but cannot find anything that would support that hypothesis. My slide and microscope aren’t sterile and I wasn’t overly particular in handling it from the screened funnel to some toilet paper to the slide. And I have been taking the urinary analgesic that makes your urine Easter egg dye orange. But these things don’t appear to be from contamination, they appear to be partially enveloped in the stone with random bits poking out of the crystals here and there. Also they were stationary. Nothing moving or wiggling. They were not uniform in shape and size either.

    Have you ever come across something like this or do you have any insight what it might be? As gross as it may be, and maybe a smidge concerning, I really am interested in learning what it might be. I’m fascinated because it goes against the expectations I have of urinary waste and stones in general. Thanks for taking the time to answer questions for me and the others, it’s very considerate and I appreciate it.

    • Fredric L Coe, MD

      Dear Sarah, If you make uric acid stones, you can stop them from forming. That will ruin your collecting but stop any pain and – I might say – dangers from the stones. Under any microscope stones are lovely, being crystals; their shapes like the stars make us think of things, too, so we can see in them our dreams, and our fantasies. As for you, stop the stones by reading the article and doing what is says. Thanks for a wonderful post, Fred

  3. Emily

    Hi I have a question,
    In august of 2020 I had a neg-coag staph infection, was given cipro for 5 days and the symptoms never fully went away. Currently I have pelvic pain and pressure, lower back pain and aching during and after peeing along with a weak stream. Two days ago I passed a soft yellow stone with mild pain. I have done some research and it seems it could be a struvite stone? I am still in pain since though. Urine tests show no infection. Thank you for your help in advance

    • Fredric L Coe, MD

      Hi Emily, Have the stone analyzed. If it is struvite you need special handling to prevent more problems. The 24 hour urine can help, struvite forms in urine that is very alkaline (high pH) and also has a lot of ammonia in it. Regards, Fred Coe

  4. Lori Ann

    Hello. I just received an analysis back of a “stone”. They said it was organic material and were not sure what it was. I will be having surgery soon since I have several large stones in both kidneys. Any idea what organic material may be?
    My doctor will discuss it with me at my next appointment. But until then, what are your thoughts?

    • Fredric L Coe, MD

      Hi Lori Ann, Not rarely a stone will form with so little crystal that all you can find in a routine analysis is the matrix protein that holds the stone crystals together. I suspect other stones will eventually show the stone. Alternative possibilities is a blood clot, tissue from the kidney. Regards, Fred Coe

  5. Paul K.

    I’ve had a calcium oscillate stone in the past, Now the stones Im passing are soft, some are pink some look like blood clots, but they look more like tissue, Dr. said caused by infection but I dont have infection, From what I’m reading they may be matrix stones? I dont know if Im getting enough information from my Dr.

    • Fredric L Coe, MD

      Hi Paul, I would be guided by your physician. If infection is causing clots or loss of tissue it is a serious infection, and we must rely on her/him to fix it. If you are not infected, that would imply an error of your physician, unlikely but also very important and pointing to a need for some additional medical help. Regards, Fred Coe

  6. Emma

    Hi I have been experiencing recurrent upper uti symptoms after starting topirimate for migraine prevention. Uss kidneys are ok but I’m concerned I may have developed kidney sludge. I have stopped the topirimate. Should this clear itself?

  7. Matt

    Hi Doctor,

    For the past 3 years I have experienced episodes that occur seemingly ever 3-4 months, they started when I was 19, and I have been to multiple different urologists, given samples of these “stones” to be tested, and have gotten no results, in fact, the last one said he hasn’t really seen anything like this.
    When this occurs, I pee out upwards of 20 small mushy stones that when I pick up and rub my fingers over, they dissolve. Some can get as big as a pencil eraser, some are very small. Each time I have this as mentioned above, I will pass over 20, and I quickly drink lots of water to flush my system and then it’s over. They are typically white or very light yellow in color.
    The first doctor I went to for this 3 years ago, ruled it as a UTI and I was treated for that. It did not stop occurring so I continued to schedule appointments (which takes months to get in). I had an ultrasound done about a year and a half ago which came up empty. In April 2019 I had a scan done with iodine which also showed nothing. I was able to present a sample in my urine to one of the doctors but when he tested it, he stated that it just fell apart like they typically do when enough pressure is applied. Do you have any advice or thoughts on what this could be and what my next steps should be? I am currently at a loss after the last visit.

    Thank you so much in advance, I hope you see this

    • Fredric L Coe

      Hi Matt, So called ‘Matrix stones’ are well described. This link to page one of a J Urol article described what you found. They usually suggest infection so perhaps your physicians should check for that. In some cases these are lightly mineralized and reflect stone crystal formation but the crystal part is too slight to sense. ANalysis by infrared spectroscopy – the common commercial stone method – may yield the crystal. 24 hour urine testing is in order to see if your urine harbors stone risk factors. Regards, Fred Coe

    • Chris

      Hi Matt,

      Did you ever figure out what this was? I am dealing with a similar issue.



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