Chapter Three: Coping With Confusion

Among the thousands of comments on this site, this one theme rings out.

Patients Are Confused

Many patients just have no idea about what to do. They suffer from confusion.

They have stones, one or many. Surgeries occur, or not. CT scans show this number of stones, or that number. Physicians may say contradictory things, or things that seem contradictory. And all the while new stones may form, more pain attacks may come, and lay to waste life otherwise spent in pursuit of work and family happiness.

As a way out, people seek remedies, on the web, from friends, from physicians, of course, and often they do not work. Or, they do work but seem not to.

The painting, Taking the Census, by Francis William Edmonds (American, Hudson, New York 1806–1863 Bronxville, New York) 1854 resides in the Metropolitan Museum in NY. The new census law required people answer a list of questions that clearly caused confusion in this family. The artist was well known for his genre paintings in the style of earlier Dutch master painting.

I Have Not Made Things Clear Enough 

I call all of this confusion. And most of the confusion does not need to occur. This site already has on it more than enough information to guide patients to proper stone prevention, even to effective ways to use the invaluable and limited time their physicians can offer them.

But I have failed in the one crucial act – a way in, a simple laying out of what to do in an order people can clearly see and take up into use.

In other words I have said a lot about why to do this or that, but not enough about what and how to do if you are a stone former hunting for a way to prevent them.

What Do We Do First?

We do not hunt around for an easy fix or a home remedy.

Let’s start wherever you are.

Perhaps you have first discovered you make stones. Or you have made stones for years and cannot find a way to stop them. Maybe they have stopped but you have an underlying disease no one has diagnosed.

Wherever you are, the beginning is the only place to start at.

If stones have just started, do not rush into this or that remedy or diet – begin at the beginning. Stones are a chronic condition. They may have manifested themselves today but no doubt they formed some time ago.

Kidney stones are more like a symptom than a disease. They result from abnormalities in the urine, or sometimes the kidneys or even the body in general. Think of them like fever, or cough, or weight loss. We do not ask grandma, our neighbors, office friends. At the beginning we need doctors.

But even before we get our physicians involved we need to think carefully about the most important first question.

Is There A Beginning?

Do You Make Stones?

Pain and urinary bleeding can seem like stones and be something else. You only know you form stones if someone sees a stone.

You could pass it in urine, and that is a sure proof. Physicians can see it or them on a CT scan. Objects in kidneys that produce ‘shadows’ on ultrasound scans are likely stones, but at the beginning I require a CT and really see them.

But if you never saw one, and your physicians never saw one, you might not make stones at all and have some altogether different problem.

If no one sees a stone, it is up to your physician to figure out what causes your symptoms, but it is not reasonable to diagnose kidney stone disease.

Do You Have Crystal Attacks?

Crystals can form and cause pain and urinary bleeding that mimic kidney stone passage. They mimic kidney stones because they are like kidney stones – crystalline objects that irritate the ureters and bladder, and cause bleeding. The crystals mostly elude CT scans and ultrasound scans. Rarely the side with pain can seem slightly dilated as if obstructed briefly, because it was.

Do You Form Abundant Urine Crystals?

Have your morning urine checked.

Because of onerous government regulations concerning any laboratory procedures, most physicians no longer use microscopes themselves, but routine technicians will identify them if you provide a timely urine sample. Everybody can form some crystals. Those whose crystals cause pain or bleeding produce abundant crystals.

But, abundant crystals may not cause your symptoms. Just they alone are not enough.

Do Crystals Cause Pain and Bleeding?

The only proof is to see the crystals in the urine during or just after an attack.

Crystal attacks with pain and often bleeding are enough like stones I accept them as part of the disease and in need of the same prevention we use for stones. If you have pain attacks worthy of diagnosis and treatment, they warrant enough repeated urine analyses to be sure.

Urinary Bleeding Demands a Diagnosis

Your urologist will invariably recommend a brief diagnostic cystoscopy and a renal CT to be sure bleeding is not from cancer. It is during that evaluation stones may be seen. Even in a proven stone former, one needs this kind of diagnostic checkup over the years. The matter is outside my immediate concerns as physicians always attend to it.

Stop Here If Things Are Not Clear

Do not proceed to elaborate kidney stone testing or treatments or remedies from the web if you do not know if you really make stones or crystals. You will be chasing shadows. Perhaps, focused on stones and crystals that do not exist you and your physicians will miss something else that causes symptoms and could be important to know about.

Until you know for sure stones or crystals cause your troubles there is no beginning here. The problem lies elsewhere, in the primary diagnosis, the cause of your symptoms.

Here Is the Beginning

What Are the Stones and Crystals Called?

You know you form stones or that crystals cause your symptoms. That is a necessary requirement. The next step is to name them.

Here are the key articles to read right now. Read them in this order.

What Kidney Stones Are

Kidney Stone Types 

These articles tell you about the central role of crystals in kidney stone disease. Crystals make stones what they are. The types of stones are simply the types of crystals in the stones. Crystals are defined precisely, by their structures of atoms and molecules into specific patterns of attachment – like macrame. If you have stones, the type is central to all of your care.

You Read About Stones, Now What?

You know enough to understand the problem. Whether or not you now know what your stones or crystals are, you are ready for the next step. That step is to understand the rudiments of stone and crystal production.

I know this step seems arcane and a sideshow but it is not. Supersaturation is what makes all crystals. It is what can guide successful treatment. So put up with a bit of detail. Become informed so you can cope well with the complexities of your evaluation and prevention efforts.

This one article introduces all the ideas. At the end it offers a walking tour that can add a lot if you have the time. The site has over a dozen articles about supersaturation you can explore over time. But right now, read just this one and be sure you fully understand what it means.

That meaning is simple: If you make stones or crystals, your urine supersaturation is too high in relation to those crystals and must be lowered.


Do not jump ahead. Things get more complicated and you need a stable base of understanding. Read this article, read some of the others if you want to. Then, move on.

You Read About Supersaturation, Now What?

We move on, into the tall grass, into the thicket of the wood, into the shadows.

Don’t Assume Things

I have heard and read hundreds of times that stones were because of X or Y and therefore this diet or that diet will prevent them. Some patients and physicians assume a lot of water is enough even though the only water trial, of people who had formed only one calcium oxalate stone, showed 12% with a recurrence over five years.

Think about that. Twelve percent in five years is a rate of 24 percent per decade, and stones typically begin in the thirties or forties.

People who form stones harbor risks like hypercalciuria, low urine citrate, high urine oxalate, abnormal urine pH in dizzying combinations. You can look these up on the site.

Some have systemic diseases like primary hyperparathyroidism, renal tubular acidosis, primary hyperoxaluria, or an occult disorder of intestinal absorption. You do not know what you have until you get your blood and urine tested properly.

That is why you need to follow the Five Steps.

Follow the Five Steps

This article lays out the whole of stone prevention. It details what you need, in what order, and why. I wrote it as the capstone to the whole site in terms of how to use the information to achieve prevention.

The Five Steps to Stone Prevention 

The five steps will inevitably bring you to the right place if you skip none and execute each one properly. I know your physicians must do some of it for you, but you can see to your care and ask that everything be taken care of.

The article emphasizes the huge role patients play in getting their own care.

It also makes clear that your laboratory reports are not in Attic Greek but in common numbers you can read and be guided by.

Organize for Your Medical Visits

Your physicians are essential but busy and sometimes even distracted by the current time demands put upon them in recent years. You need to do everything you can to put what they will need in front of them so they can do the one thing only they can: Integrate everything into a specific diagnosis and offer a treatment plan.

The first of these includes systemic disease diagnosis when present. This is critical and unique to physicians. It also includes judgment about how best to lower supersaturation given your unique situation and especially stone type.

How to be a Successful Kidney Stone Patient

This is a wonderful article that not enough people use. It has lists and hints and ideas about how to use the time physicians have to give you. I wrote it from my side of the wall. If you use it, you will benefit.

Above all this article has in it the prevention cycle – the year over year re-testing and treatment modification one needs to keep prevention in step with changes in you brought on by age, or life.

Read This Homely Summary and be Sure

The five steps and successful patient articles are big and complicated. I wrote this simpler wraparound article to do what the title says:

Putting It All Together

Before you see your physician, but after you read the prior articles, read this one. It uses the others as reference points and summarizes the key points.

Integrate Your Results and Move Forward

Think about the six articles, read them over. Do what they say in terms of gathering things together, getting tested, looking at your own results. Then plan for the crucial physician visit that will begin your kidney stone prevention work.

Do things in that order. Skip nothing.

Separate Stone Management From Stone Prevention

The Surgical Alternatives are from Your Urologist

What to do about what stones you have is all about surgery or not, and if surgery what kind. Intricate and entirely a matter for urologists, no site can guide you except in general. For stones already there you have four options: Nothing, shock wave lithotripsy, modern digital ureteroscopy, and percutaneous nephrolithotomy – an actual surgical entry into the kidney through the back.

This article is a good review of ureteroscopy, the most recent modality and the most preferable, to my taste, when usable.

Ureteroscopy – Background and Technique

But choice of modality is local – to you and your urologist.

Prevention Is Separate From Stone Management

Even if you use your urologist for both prevention and stone management, do not try to accomplish both in one visit. Separate them as they have little or no relationship with one another.

The one is about surgery or not, and what kind of procedures are best.

The other is about causes of stones and their long term reversal.

Each is a complex matter and needs its own time.

Find Your Phenotype

At the end of your evaluation you will fit into one of the phenotypes of kidney stone formers. The next chapter speaks about them. That phenotype guides all of your other reading on this site and offers entre into what is known about your condition. In fact, it names your condition.

Look To The Future

The article on how to be an effective kidney stone patient How to be a Successful Kidney Stone Patient points forward. Never leave it to one side, but look at it every year. Be sure about the prevention cycle – that you have engaged it and are engaged in it. 

If stone events occur despite treatment, and you read this site, you will know to separate passage of old stones from formation of new ones. You will know that new stones mean supersaturation is too high in relation to the crystals in your new stones. You will know to lower it further.

As the causes of your stones become clear you can read on this site about virtually all of them, and in some detail. You will come to know, and you will find what you need.

Keep Reading

It takes a long time to absorb all you can know about kidney stones and their prevention. I believe an educated patient is a safer and more successful patient, and because I believe that way I urge you to read whatever you can about whatever it is you have as your cause of stones.

Because I cannot know what that will be, this is the end of my present story.

But you will know, and the rest of the site awaits you.

30 Responses to “Chapter Three: Coping With Confusion”

  1. Rhys James

    Dear Dr. Coe,
    Thank you for your comprehensive book on Kidney stones. My background on Chemistry is many decades past. I wanted to ask you to clarify my confusion on Green Tea and Oxalate. There is confusion in the literature that promotes Tea with an 11% reduced probability of future KS development. Yet all teas are high in oxalate. Thus some stones are formed from oxalate and Green Tea contains Oxalate (10mg/120ml) is this level of Oxalate in Green Tea still beneficial for reducing Kidney stones?

    • Fredric L Coe

      Hi Rhys, I gather you have stones and they are calcium oxalate. Is your urine oxalate the main abnormality causing your stones? Is tea necessary for your happiness or will coffee – reduced stone risk – acceptable? If stones are calcium oxalate and urine oxalate is abnormally high – >25 mg/d is the beginning of risk – and tea essential, use the green one. If you add milk or cream to the tea the calcium will suppress oxalate absorption. 24 hour urines are essential here, as nothing else will disclose that your beverages and diet and genes have conspired to do to make stones form. Regards, Fred Coe

  2. Gwennie Elliott

    I am 61, I have a 5mm kidney stone, been in lots of pain in the groan and left side of back, went to doctor was sent for a ct scan and was than told of the kidney stone, from there was sent to a pain mangment doctor whom put me on 300mg of Gabapentin {Neurontin} 3 times daily this has made me vary tired, and hard to function need to lie down often catch myself nodding off. Trying to find out what else I can do to help myself with the pain and disconforter instead of this medication! I would appericate your expertice, PLEASE give me an Idea of what I should do or if I am seeking the right direction! I have been drinking lots of lemon water. Not eating sweets, or sugar! 1 cup decafe coffee a day the rest is lemon water. No spinach, are tomatoes okay, eating cheeses, chicken, shrimp. Going to contact my Urologisto Monday.

    • Fredric Coe, MD

      Hi Gwennie, given so much pain, and possibly from the stone, perhaps surgery might be worthwhile. But this is entirely a matter for your surgeons. Stone prevention will do nothing for the stone in your kidney, but will help prevent more stones. The article you commented on is a good introduction to prevention and warns against trying to pick a remedy without a proper evaluation as to the cause of the stones. Regards, Fred Coe

  3. Don Donnelly

    As I write with my 2nd stint in me, I realize I have not had the pain and trouble which many of the people who have commented. I consider myself lucky. Your site is wonderful. On another site they made the comment that protein from non-meat sources does not appear to increase the risk of stones. I do not think they have the scientific resources that you have and the internet can be a source of “fake science”. I would like this to be true because we each a lot of beans and tofu in place of meat. Thanks

    • Fredric Coe, MD

      Hi Don, As it happens, I am just reviewing a new paper about protein for my site – not ready yet. I do not think any proteins matter much from their data. But they do not specially consider protein extracts and concentrates – like shakes. The chapter you are reading matters – be sure you know what is wrong with you and act accordingly. So many factors can promote stones, you need to be orderly and track them down. Regards, Fred Coe

    • jharris

      Hi Don,

      Eating too much beans and tofu can certainly increase your oxalate levels. Do you need to lower oxalate? If so, you must really watch your portion size of beans and think about nixing the tofu as soy is terribly high in oxalate. Don’t forget to eat your daily required calcium!

    • jharris

      Hi Don,

      Eating too many beans and tofu can certainly increase your oxalate levels. Do you need to lower oxalate? If so, you must really watch your portion size of beans and think about nixing the tofu as soy is terribly high in oxalate. Don’t forget to eat your daily required calcium!

  4. Teri Rainsberg

    I am confused!! I have MTHFR – which means I can’t process Folic Acid – so I can’t have processed foods (breads, pastas, cereals). I was told not to do gluten. I have Lupus and Hypothyroid. I had a 1.1 cm stone removed last month and I’m scheduled for removal of a .8 and .6 next week. I was given a list of foods and where they stand on oxalate and told to eat between 40-50 mg a day. I did the 24 hour test and my Calcium was 448 and my oxalate was 47. I am reading everything from your site and I also am on the Facebook page for Jill. My question is – where do I start? I was eating healthy all these years and now am told that I can’t eat any of those foods. I know Jill has training videos, but with the surgery last week and the one next week, monies are tight for this one income family. I want to do this right, but I’m so afraid that with all the restrictions I will cause other health problems. Where would you suggest to start? What would be the most important first steps? Thanks in advance!!

    • Fredric Coe, MD

      Hi Teri, The first step is low sodium – cheap and good in general for your health. Very stringent low oxalate diets are rarely needed if you can manage a high calcium intake, but this latter requires first of all a low diet sodium – 1500 mg is ideal. Your stone report gives your urine sodium which is more or less your diet sodium. It is in mEq/d, and 100 mEq/day is 2300 mg. Begin there. RE-test to be sure you got there; urine calcium should have fallen a lot. Feel free to come back here. Regards, Fred Coe

  5. Alex Pavchinski

    What is the latest research on Hydroxycitrate and its effect on calcium oxalate stones? I have read several articles that say this is a promising treatment.

    • Fredric Coe, MD

      Hi Alex, No trial, an over the counter or health food supplement, so who knows? But I reject monopolar treatments because stones are a sign of more wrong – patients can get bone disease, kidney disease, hypertension, and all mainly because our present diet does not work well for them. Better to change it, reduce urine stone risks and also act against the other diseases, too. Regards, Fred Coe

  6. Christina Stephenson

    Thank you for this information because it really helps to understand why I am experiencing confusion over my kidney stones to some extent. Do you have any information or know of any research that indicates that kidney stones are often associated with the kidney disease IGA Nephropathy? I was diagnosed with it many years ago and was told that because of its slow progression I would make it to retirement without too many problems (which I have!). It appears as if it has been episodic and when I have gone for emergency pain management at a hospital when passing a stone I have been told by two doctors that kidney stones are often associated with the kidney disease of IGA Nephropathy which I was unaware of. I have had a stone analysed just recently and it is a calcium oxalate stone so I am now seeing a dietitian to make changes to my diet.

    • Fredric Coe, MD

      Hi Christina, Thin basement membrane disease is associated with hypercalciuria; I found a case of a child with hematuria ascribed to hypercalciuria who later proved to have IGA nephropathy; a comment to a review article about IGA nephropathy points out that hematuria may often arise from hypercalciuria and confuse the diagnosis. But no one has linked IGA nephropathy itself to cause of stones. I presume you have stones and IGA nephropathy and I would pursue the evaluation as would anyone else. Since stones themselves can cause kidney injury their prevention is very important. Regards, Fred Coe

      • Christina Stephenson

        Thank you. Throughout my life I have always had a high level of blood cells in my urine tests when put under a microscope even when the urine appears to be absolutely clear to the eye (hematuria). I have also had gross hematuria on occasions (IGA Nephropathy) and had tests done and it was also found I had an excessively high level of calcium in my urine which I was told would attribute to kidney stones. So it sounds like IGA Nephropathy and kidney stones. As you suggest time to pursue the evaluation and a visit back to the Kidney Physician for a start. Many thanks again for your help some things are becoming clearer.

        • Fredric Coe, MD

          Hi Christina, I presume you have both idiopathic hypercalciuria and IGA nephropathy, but the former requires testing to prove up. So pursue the evaluation. Best, Fred Coe

          • Meg G.

            Hi Dr. Coe,
            I have Christina’s exact symptoms. Chronic microscopic hematuria (with just three instances of gross hematuria), hypercalciuria and calcium oxalate stones. Years also i was told I might have IgA nephropathy but that it wasn’t worth the diagnosis (biopsy) since my kidney function is fine. Is it more likely that i don’t have IgA nephropathy and that the hematuria is simply caused by the hypercalciuria?

  7. Suzanne larrison

    I’ve had 8 stones calsium oxide my dr says to drink large amounts of lemon water what is your option of a defective para thyroid in respect to forming multiple stones #8 is getting shockwave lipotripsy tomorrow I’ve removed tea from my diet and eat very little dairy I was also told Spinish is also a instigator what’s your option please TY

    • Fredric Coe, MD

      Dear Suzanne, The article you are commenting to is ideal for you. It sets out what you need to do to get prevention. Parathyroid disease is diagnosed from blood tests. Your low calcium diet is exactly wrong for your bones and not helpful for stones. Spinach is indeed a risk because of oxalate. Read through the article and check off what you know and then do the steps that are highlighted in blue – links. They will lead you to proper diagnosis and stone prevention. Regards, Fred Coe

  8. Kathy Tessner

    I am confused, my husband is in nursing home rehabilitation facility, he has been in excruciating pain, had XRAY, found out,small kidney stone, on top of that ,he has a small gallstone, from 2 years ago, too tiny to operate on. Plus a small cyst on his pancreas, 2014 had a VP SHUNT INSERTED INTO the skull, diagnosis normal pressure hydrocephalus, does this kidney stone, cause him to be so agitated, and confusion, and paranoid? On antibiotics as of yesterday 9/14/27, penicillin. Pain like every 10.mins, and has a catheter since 8/9//17,had surgery from cellulitis, and Sepsis, in right groin of leg, ,also got a uti, infection, and he is diabetic, please i need answers, thank you.

    • Fredric Coe, MD

      Hi Kathy, You describe a very complex set of medical issues: pain, kidney stone, gallstone, VP shunt, urinary catheter, infection that may be just groin cellulitis or urinary or both, diabetes. He is confused and paranoid. This is high level inpatient care. Obviously a diabetic will do less well when infected, and his catheter – associated UTI and cellulitis no doubt can worsen mental status. I doubt the stone plays a role right now unless it is obstructing the ureter or kidney. On a practical level, only his physicians can sort all this out – anything I could say would be too derivative. Let’s hope they can get things treated. Best wishes, Fred Coe

  9. Ryan Tol

    I am so confused I was hoping you could help me. I am 41 I have had five and 6 mm stones for five times over the past 10 years. I have had one in 2 mm stone several times. I have high blood pressure high cholesterol and here are my numbers from my 24 hour urine analysis. Every 3 to 6 months I have a small stone and it’s almost impossible for me to live like this anymore. My urine volume is 2.32, my SSCAOX is 8.43, urine calcium 421, urine oxalate 48, urine citrate 267, SSCAP .60, 24 hour urine pH 5.404, SS uric acid 1.89, urine uric acid 0.857. I was put on a low calcium low actually low-sodium diet I cannot figure out what I should be eating on a daily basis it’s very difficult. Please help

    • Fredric Coe, MD

      Hi Ryan, You do not say what your stones are. The high urine calcium and oxalate could produce calcium oxalate stones, the low pH uric acid stones. As I do not have a proper medical knowledge of your situation I can only offer some ideas for your physicians to consider: Low sodium diet 1500 mg, high calcium intake of 1200 mg daily with the main meals, potassium citrate to raise the urine citrate and pH, and chlorthalidone to further lower urine calcium and incidently your blood pressure. Let me make clear this is not medical advice, it is a set of suggestions your physicians may with to consider in light of their immediate knowledge of your particular situation. If your stones are calcium, here is the rationale. If uric acid, this article. Regards, Fred Coe

  10. Gretchen Schaffer

    You are a godsend to so many. At the age of 70 I am now at the beginning of my journey to solve my own stone issue with the help of Dr Koopman at Swedish Covenant in Chicago. The true emotional relief came when a young resident Dr. Alieva turned me on to your site. Years of anxiety are now over and I see the resolution in sight due to your clarity and guidance. The worst part of the journey is the confusion and the anxiety, and now that is over. Chapter Three here is the info we all needed to feel confident. Thank you for sticking with us. There is no way to thank you enough for your work. It will help so many and alleviate so much pain.


Leave a Reply