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How to collect a urine sample properly for testing (UPDATED August 2023)


Man collecting a clean catch urine sample
It is essential for lupus patients to regularly collect an accurate clean catch urine sample

August 2023 update:

Other causes of elevated protein are added to the blog post at the end of the article

Why do lupus patients need to give a clean catch urine sample every 3 months?

– 45% of systemic lupus patients will develop kidney inflammation (lupus nephritis)

– Lupus nephritis causes NO SYMPTOMS early on. We want to catch it at this early curable stage

– Ask your doctor to order a urinalysis with a random urine protein creatinine ratio each time

-If the result is 500 (or 0.5) or higher, repeat it after hydrating well for several days and repeat first thing in the morning (see below)

-If it remains at 500 (0.5) or higher, a kidney biopsy is warranted to figure out what is going on, reach a correct diagnosis and get you proper treatment

-For a great review on lupus nephritis management and screening, see the European League Against Rheumatisms Lupus Nephritis Guidelines.

Doing a clean catch urine sample wrong can cause false results

Around 40% of systemic lupus erythematosus patients develop kidney inflammation (nephritis) and need to give a clean catch urine sample regularly. It is always essential to give a proper clean catch urine sample to ensure the results are accurate.

Some groups get it more often, as high as 80% in Afro-Caribbean women and 50-55% in African American women
Finding excess protein in the urine (proteinuria) is how we identify lupus nephritis at its earliest stages.

How can the urine sample be inaccurate?

If there are white blood cells, red blood cells, and other substances contaminating it from the vagina or foreskin, this can cause an artificially high amount of proteinuria.

If you collect it after exercising or in the late morning or afternoon, it can be artificially high (orthostatic proteinuria)

How to get a clean catch urine sample (PRINT THIS OUT AND KEEP IT HANDY):

Why this is important: 

If you get into the habit of doing this correctly, you will save yourself from having to repeat it or from having to collect an unnecessary 24-hour urine collection (which is cumbersome to do)

“What is the best time to take a urine sample?”

– Always try to collect your clean catch urine sample first thing in the morning (either the 1st or 2nd void)
– Hydrate. Drink at least 8 glasses of water daily for a few days before the collection (unless your doctor has you on a water restriction)

Collect a mid-stream, clean catch urine sample:

– 1st wash your hands.
– Carefully remove the lid from the urine sample cup (making sure not to touch the inside of the container or cover) and lay the cover with the inside section facing up.
– If you are giving a urine culture as well, to make sure you do not have a urinary tract infection, use a sterile cup.
– Place the cup on an easy-to-reach surface.

How to give a urine sample female:

-Pull apart the labia (if you have them) with one hand.
– Using your other hand, you wipe the urethra three times with three sterile wipes front to back. This is important. If you wipe back to the front, you can introduce bacteria around the anus that can potentially give you a urinary tract infection.

-Continue to keep the labia with one hand and grab the cup with the other hand.

How to give a urine sample male:

– retract the foreskin (if you have one) with one hand.
– Using your other hand, you wipe the urethra three times with three sterile wipes. Keep the foreskin retracted with one hand and grab the cup with the other.

Next steps giving a urine sample for both sexes:

– You then urinate the first couple of seconds into the toilet (this gets rid of any bacteria that may have been in the urethra), and then urinate into the cup to the fill line.
– You should empty the last part of your urine sample into the toilet again (which is why the term “midstream”). You should immediately put the lid securely on the cup, ensuring not to touch the inside of the cover or the container.
– Make sure and place the lid securely on the cup before flushing the toilet to prevent contamination from aerosolized droplets from the toilet (thanks to ANON’s recommendations in the comments section for this great recommendation).

“Can I give a urine sample with my period?

This is an important question. If you are asked to give a clean catch urine sample at a time when you are having any blood at all during your period, tell your doctor or the lab technician that you need to return on a day when you have no more bleeding at all. If red blood cells get into the urine sample, it will cause inaccurate readings of the amount of protein (it will be falsely elevated) and an increased number of red blood cells.

What if my urine protein is increased?

If the urine protein to creatinine ratio is more than 500 (or notated as 0.5 in some labs), we repeat the test and ask that the patient to make sure and drink lots of water and make sure the sample is the 1st or 2nd void of the day. If this repeat test is greater than 500 (or 0.5) a kidney biopsy is recommended to see if it is due to lupus nephritis or not. If it is lupus nephritis, then the biopsy can tell us which type it is, how bad it is, if it is treatable, and how much permanent damage has already occurred (If any).

If it is less than 500 (or 0.5) a biopsy is usually not done because it is unlikely that the biopsy will show lupus nephritis requiring immunosuppressant therapy. We typically watch it more closely and ensure the patient works on keeping their numbers perfect (blood pressure, glucose levels, cholesterol) and avoid things that can harm the kidneys (like NSAIDs and Chinese herbs).

However, an exception is if I have a patient with other risk factors for lupus nephritis, like a high anti-dsDNA, low complements, and a high anti-C1q antibody, or if the kidney function is lower, then I will get a kidney biopsy if the protein level is elevated but less than 500 (or 0.5).

Other causes of elevated protein in the urine

There are many other things that can cause elevated protein in the urine.

Exercise and standing or sitting for quite a while before the test can elevate the protein and is not a concern.

Other diseases can also elevate the protein level. These include things such as scar tissue from other disorders, damage from medications (like NSAIDs like ibuprofen and naproxen), and hardening of the arteries. Sometimes we can successfully guess the cause in the absence of a biopsy. An example would be a patient who has had a long history of elevated blood pressures (greater than 120/80) and then develops a mildly elevated protein level. The most likely cause in this scenario would be damage to the kidneys over the years from the high blood pressure. We call this hypertensive nephrosclerosis (fancy medical words for high blood pressure causing scarring of the kidneys). The treatment is to work on perfect blood pressure control.

There are a few lupus-related kidney problems that are not included in the classification of lupus nephritis (which classifies the lupus nephritis from class I to class VI). These other lupus kidney problems include inflammation of the blood vessels (vasculitis), damage to the kidney cells that form the microscopic kidney filters (lupus podocytopathy), and microscopic blood clots from antiphospholipid antibodies (antiphospholipid nephropathy). The first two are treated with immunosuppressants and the latter is treated with blood thinners. All forms of lupus nephritis plus these last three entities also require hydroxychloroquine to help.

PRINT this out and keep it handy


For more in-depth information on how to properly collect a urine sample and what the results on the urine lab slip mean:

Read chapters 4 and 12 of The Lupus Encyclopedia, edition 2

Look up your symptoms, conditions, and medications in the Index of The Lupus Encyclopedia

If you enjoy the information from The Lupus Encyclopedia, please click the “SUPPORT” button at the top of the page to learn how you can help. 

What are your comments and opinions?

If you have lupus nephritis, what has your experience been? What do you recommend for other patients?

Do you have any questions to ask Dr. Thomas?

Please click on “Leave a Comment” above to comment.

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Don Thomas, MD, author of “The Lupus Encyclopedia” and “The Lupus Secrets


The Lupus Encyclopedia

​Fanouriakis A, Kostopoulou M, Cheema K, et al. 2019 Update of the Joint European League Against Rheumatism and European Renal Association–European Dialysis and Transplant Association (EULAR/ERA–EDTA) recommendations for the management of lupus nephritis. .Annals of the Rheumatic Diseases 2020;79:713-723.


  1. Just in case flushing could aerosolize other people’s germs that are hanging out in the toilet, I make a point to NOT flush the toilet until AFTER I’ve put the cap on the urine cup, put the cup into the little metal box in the wall, and closed the door to the little metal box. I don’t know how likely this is, but I don’t want to be told I have a UTI and be put on antibiotics unnecessarily due to someone else’s E. coli (or some other bacteria lurking in the toilet from people who used it before me) contaminating my urine sample. I never thought of this until I had to give a urine sample at my GYN’s office and they had very detailed instructions in a fancy frame sitting on a bathroom shelf right with all the necessary supplies … and their instructions said to put the cap on the urine cup before flushing the toilet… and then I thought about why they might have said to do things in that particular order.

    • I love that ANON. I am going to add that to the instructions when I publish the 2nd edition of my book. E coli does get aerosolized with flushes, so it makes sense to add this recommendation.

  2. […] asks you to do a urine sample every 3 months (hopefully) – This is why you should do a frequent urine sample. The faster it is diagnosed, the faster it is treated, the higher the chances for remission – […]

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