Kidney stones and urinary infections

Urinary infections and kidney stones can be related in two important ways. Infections can be the direct cause of stones or can develop in a patient with a non-infection related kidney stone.

Infections cause kidney stones in about 15% of stone formers.

Chronic infection in the kidney by certain bacteria can directly cause kidney stones. These bacteria all produce an enzyme known as urease. Urease is an enzyme that causes hydrolysis of urea, a common substance in urine. This produces ammonium and hydroxyl ions. Alkaline urine results and in combination with ammonium and phosphate ions, leads to the development of magnesium ammonium phosphate stones, also known as struvite stones. Infection stones can also contain carbonate apatite and monoammonium urate. These stones can become quite large and fill up an entire kidney. They are the most common cause of so called “staghorn” stones.  Picture of a staghorn stone.

Treatment of infection stones involves clearance of all stones and antibiotics. Removal of all stones is important because they can contain bacteria, which will not be cleared with antibiotics alone.

Patients with infection caused struvite stones usually present with chronic infections and chronic low-grade flank pain rather than with the acute flank pain more commonly associated with other types of stones.

Infection can develop in a patient with a non-infection caused stone.
When a normal kidney stone causes obstruction, infection does not usually occur. However, in some cases, the lack of urine drainage and inflammation from an obstructing stone can lead to development of a urinary tract infection. 10% of hospital admissions for kidney stones are for an infection complicating a kidney stone. Patients in this situation will often have severe flank pain and fevers.

Obstructing ureteral stone and infection

CT scan of an obstructing stone with kidney infection.

An infection “behind” an obstructing stone is often an emergency because the body has difficulty clearing these infections and because antibiotics often cannot not reach adequate levels due to the decreased blood supply and urine flow that occurs whenever a stone causes obstruction. In these cases, urgent drainage with either placement of a ureteral stent by a urologist or a percutaneous nephrostomy tube by a radiologist is often required.


  1. Thomas et al, Concurrent urinary tract infection and stone disease: pathogenesis, diagnosis, and management. Nature Clinical Practice Urology, 2008.
  2. Brown, Management of urinary tract infections associated with nephrolithiasis, Curr Infect Dis Rep, 2010.


About Dr. Mike Nguyen

Mike M Nguyen, MD, MPH, is a urologist and an Associate Professor of Clinical Urology at the Keck School of Medicine of USC in Los Angeles, CA. He specializes in the treatment of kidney stones with both surgery and dietary prevention and the in the treatment of kidney and prostate cancer using the latest robotic surgical approaches. He sees patients at clinics located in Los Angeles, Pasadena, and La Canada, CA. He is the founder of the website.
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9 Responses to Kidney stones and urinary infections

  1. a says:


    Is it possible that embedded stones – after many lipotorpsies- casue inflammtion in not only the kidney but via the bacteria also in the chest? My husban has recurrent inflammation , then chest infections..

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  4. christie says:

    Please help!! I have been trying to pass a stone since Tuesday evening. I went to the ER last night and I have white cells, red blood and small crystals in my urine. No CT scan was done. Sent me home to treat infection and stone. I contacted my urologist today, following ER docs instructions. They can’t see me til next friday! I am still in pain after taking 10 MG toridol and 10 mg of hydrocodone. My back and front both hurt! I asked them what I should do if I don’t pass it before Friday and I get worse. Their answer was to go back to ER or talk with my primary doctor. The type of stones that I have been forming are 10% calcium and 90% dahllite. I’m lost on what to do! Please help! !!

  5. shannon marshall says:

    I just have one question involving kidney stones. I have two kidney stones in my left kidney. Ever since my radical nephrectomy in june of 2011, I suffer from what seems like chronic urinary tract infections. could these two minor stones be causing this issue to flare up? My urologist is two hours away,and not readily available at times of issue flare up. Is there a natural way to eliminate these stones on my own? And how effective is this method of kidney stone elimination/

  6. Kathy Boyle says:

    Recently had a blood in my urine and what I thought was a pulled muscle on the right side of my back. Dr. sent for CT scan and thought I would pass a stone. Came back with numerous non obstructing stones. One staghorn in right kidney (2×1 cm), and the largest in the left kidney at 6mm. Also have a simple cyst on right kidney. Have not yet passed anything after one month. Worst part is just the “waiting”.
    Experiencing mild discomfort – nothing really bad. Have ongoing ( 1 month) infection with one course of antibiotic and due to start another round with something different. I have been trying to research as much as possible before going to see the urologist. Pretty sure they will recommend treatment. My limited research leads me to believe treatment for the staghorn stone should probably be PCNL because of better outcome for this type of stone. Does anyone have any experience with other procedures for this type of stone? Really new to this problem, and I want to make the right choice. I am not currently worried about the left side. Had to cancel facet joint ablation in my back because of infection (which was probably just as well since kidney may be causing a lot of the discomfort). Also wonder if I should be tested for hyperparathyroid problems? I am 55 y.o. female in otherwise good health. Any advice would be appreciated! Thanks.

    • Patty Morgan says:

      Hi I am 51 years old and it’s a very long story. I have been desk
      Long with an extremely large staghorn stone since I was admitted to the hospital beginning of April this yr. I was there for 8 days just trying to get infection under control. Since then I had 4 ESWL lithotripsies on rt kidney where staghorn stone was. Got to where my pain kept getting so bad, it was constant. I could not even walk in grocery store without someone having to put me in wheelchair to take me to my car. Finally got another Dr. He immediately put a scope in me with a rapid lazer & basket & tried to grt it out. Placed a stent in which was unbearable, just had it removed today and I hate to say I’m in more pain than ever and Dr doesn’t even know if he got it. Anyway there’s way more to story. Please call me anytime day or night if u want to talk. (813)361-8460.
      Patty Morgan

  7. yvon lalande says:

    ? I got a dead right kidney ,situation at time I urinate black pee,or it clear has tap water. CT can’t find anything Should I that dead kidney remove.
    Tks you.

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