Laboratory investigations typically carried out include:

- microscopic examination of the urine, which may show red blood cells, bacteria, leukocytes, urinary casts and crystals;

- urine culture to identify any infecting organisms present in the urinary tract and sensitivity to determine the susceptibility of these organisms to specific antibiotics;

- complete blood count, looking for neutrophilia (increased neutrophil granulocyte count) suggestive of bacterial infection, as seen in the setting of struvite stones;

- renal function tests to look for abnormally high blood calcium blood levels (hypercalcemia);

- 24 hour urine collection to measure total daily urinary volume, magnesium, sodium, uric acid, calcium, citrate, oxalate and phosphate;

- collection of stones (by urinating through a StoneScreen kidney stone collection cup or a simple tea strainer) is useful. Chemical analysis of collected stones can establish their composition, which in turn can help to guide future preventive and therapeutic management.

In people with a history of stones, those who are less than 50 years of age and are presenting with the symptoms of stones without any concerning signs do not require helical CT scan imaging. A CT scan is also not typically recommended in children.

Otherwise a noncontrast helical CT scan with sections is the diagnostic modality of choice in the radiographic evaluation of suspected nephrolithiasis. All stones are detectable on CT scans except very rare stones composed of certain drug residues in the urine, such as from indinavir. Calcium-containing stones are relatively radiodense, and they can often be detected by a traditional radiograph of the abdomen that includes the kidneys, ureters, and bladder (KUB film). Some 60% of all renal stones are radiopaque. In general, calcium phosphate stones have the greatest density, followed by calcium oxalate and magnesium ammonium phosphate stones. Cystine calculi are only faintly radiodense, while uric acid stones are usually entirely radiolucent.

Where a CT scan is unavailable, an intravenous pyelogram may be performed to help confirm the diagnosis of urolithiasis. This involves intravenous injection of a contrast agent followed by a KUB film. Uroliths present in the kidneys, ureters or bladder may be better defined by the use of this contrast agent. Stones can also be detected by a retrograde pyelogram, where a similar contrast agent is injected directly into the distal ostium of the ureter (where the ureter terminates as it enters the bladder).

Renal ultrasonography can sometimes be useful, as it gives details about the presence of hydronephrosis, suggesting the stone is blocking the outflow of urine. Radiolucent stones, which do not appear on KUB, may show up on ultrasound imaging studies. Other advantages of renal ultrasonography include its low cost and absence of radiation exposure. Ultrasound imaging is useful for detecting stones in situations where X-rays or CT scans are discouraged, such as in children or pregnant women. Despite these advantages, renal ultrasonography in 2009 was not considered a substitute for noncontrast helical CT scan in the initial diagnostic evaluation of urolithiasis. The main reason for this is that compared with CT, renal ultrasonography more often fails to detect small stones (especially ureteral stones), as well as other serious disorders that could be causing the symptoms. A 2014 study confirmed that ultrasonography rather than CT as an initial diagnostic test results in less radiation exposure and did not find any significant complications.

Classically, MSK is seen as hyperdense papillae with clusters of small stones on ultrasound examination of the kidney or with an abdominal x-ray. The irregular (ectatic) collecting ducts are often seen in MSK, which are sometimes described as having a "paintbrush-like" appearance, are best seen on intravenous urography. However, IV urography has been largely replaced by contrast-enhanced, high-resolution helical CT with digital reconstruction.

Nephrocalcinosis is diagnosed for the most part by imaging techniques. The imagings used are ultrasound (US), abdominal plain film and CT imaging. Of the 3 techniques CT and US are the more preferred. Nephrocalcinosis is considered present if at least two radiologists make the diagnosis on US and/or CT. In some cases a renal biopsy is done instead if imaging is not enough to confirm nephrocalcinosis. Once the diagnosis is confirmed additional testing is needed to find the underlying cause because the underlying condition may require treatment for reasons independent of nephrocalcinosis. These additional tests will measure serum, electrolytes, calcium, and phosphate, and the urine pH. If no underlying cause can be found then urine collection should be done for 24 hours and measurements of the excretion of calcium, phosphate, oxalate, citrate, and creatinine are looked at.

Biochemical blood tests determine the amount of typical markers of renal function in the blood serum, for instance serum urea and serum creatinine. Biochemistry can also be used to determine serum electrolytes. Special biochemical tests (arterial blood gas) can determine the amount of dissolved gases in the blood, indicating if pH imbalances are acute or chronic.

Urinalysis is a test that studies urine for abnormal substances such as protein or signs of infection.

- A Full Ward Test, also known as dipstick urinalysis, involves the dipping of a biochemically active test strip into the urine specimen to determine levels of tell-tale chemicals in the urine.

- Urinalysis can also involve MC&S microscopy, culture and sensitivity

Urodynamic tests evaluate the storage of urine in the bladder and the flow of urine from the bladder through the urethra. It may be performed in cases of incontinence or neurological problems affecting the urinary tract.

Ultrasound is commonly performed to investigate problems of the kidney and/or urinary tract.

Radiology:

- KUB is plain radiography of the urinary system, e.g. to identify kidney stones.

- An intravenous pyelogram studies the shape of the urinary system.

- CAT scans and MRI can also be useful in localising urinary tract pathology.

- A voiding cystogram is a functional study where contrast "dye" is injected through a catheter into the bladder. Under x-ray the radiologist asks the patient to void (usually young children) and will watch the contrast exiting the body on the x-ray monitor. This examines the child's bladder and lower urinary tract. Typically looking for vesicoureteral reflux, involving urine backflow up into the kidneys.

The standard diagnostic workup of suspected kidney disease is history & examination, as well as a urine test strip. Also, renal ultrasonography is essential in the diagnosis and management of kidney-related diseases.

Regular X-rays often fail to show the cystine stones, however they can be visualized in the diagnostic procedure that is called intravenous pyelogram (or IVP for short). Stones may show up on XR with a fuzzy gray appearance. They are radioopaque due to sulfur content, though more difficult to visualize than calcium oxalate stones.

Chronic kidney failure is measured in five stages, which are calculated using a patient’s GFR, or glomerular filtration rate. Stage 1 CKD is mildly diminished renal function, with few overt symptoms. Stages 2 and 3 need increasing levels of supportive care from their medical providers to slow and treat their renal dysfunction. Patients in stages 4 and 5 usually require preparation of the patient towards active treatment in order to survive. Stage 5 CKD is considered a severe illness and requires some form of renal replacement therapy (dialysis) or kidney transplant whenever feasible.

- Glomerular filtration rate

A normal GFR varies according to many factors, including sex, age, body size and ethnic background. Renal professionals consider the glomerular filtration rate (GFR) to be the best overall index of kidney function. The National Kidney Foundation offers an easy to use on-line GFR calculator for anyone who is interested in knowing their glomerular filtration rate. (A serum creatinine level, a simple blood test, is needed to use the calculator.)

The diagnosis of bladder stone includes urinalysis, ultrasonography, x rays or cystoscopy (inserting a small thin camera into the urethra and viewing the bladder). The intravenous pyelogram can also be used to assess the presence of kidney stones. This test involves injecting a radiocontrast agent which is passed into the urinary system. X-ray images are then obtained every few minutes to determine if there is any obstruction to the contrast as it is excreted into the bladder. Today, intravenous pyelogram has been replaced at many health centers by CT scans. CT scans are more sensitive and can identify very small stones not seen by other tests.

Increasing fluid intake to yield a urine output of greater than 2 liters a day can be advantageous for all patients with nephrocalcinosis. Patients with hypercalciuria can reduce calcium excretion by restricting animal protein, limiting sodium intake to less than 100 meq a day and being lax of potassium intake. If changing ones diet alone does not result in an suitable reduction of hypercalciuria, a thiazide diuretic can be administered in patients who do not have hypercalcemia. Citrate can increase the solubility of calcium in urine and limit the development of nephrocalcinosis. Citrate is not given to patients who have urine pH equal to or greater than 7.

Often, aggressive treatment is unnecessary for people with MSK disease that does not cause any symptoms (asymptomatic). In such cases, treatment may consist of maintaining adequate fluid intake, with the goal of decreasing the risk of developing kidney stones (nephrolithiasis). Cases of recurrent kidney stone formation may warrant evaluation for possible underlying metabolic abnormalities.

In patients with low levels of citrate in the urine (hypocitraturia) and incomplete distal renal tubular acidosis, treatment with potassium citrate helps prevent the formation of new kidney stones. Urinary tract infections, when they occur, should also be treated.

Patients with the more rare form of MSK marked by chronic pain typically require pain management. Non-obstructing stones in MSK can be associated with significant and chronic pain even if they're not passing. The pain in this situation can be constant. It is not certain what causes this pain but researchers have proposed that the small numerous stones seen in MSK may cause obstruction of the small tubules and collecting ducts in the kidney which could lead to the pain. This pain can often be debilitating and treatment is challenging. Narcotic medication even with large quantities is sometimes not adequate. Some success with pain control has been reported using laser lithotripsy (called “ureteroscopic laser papillotomy”).

Diagnostic workup varies by the stone type, but in general:

- Clinical history and physical examination

- Imaging studies

- Some stone types (mainly those with substantial calcium content) can be detected on X-ray and CT scan

- Many stone types can be detected by ultrasound

- Factors contributing to stone formation (as in #Etiology) are often tested:

- Laboratory testing can give levels of relevant substances in blood or urine

- Some stones can be directly recovered (at surgery, or when they leave the body spontaneously) and sent to a laboratory for analysis of content

Imaging studies, such as an intravenous urogram (IVU), renal ultrasonography, CT or MRI, are also important investigations in determining the presence and/ or cause of hydronephrosis. Whilst ultrasound allows for visualisation of the ureters and kidneys (and determine the presence of hydronephrosis and / or hydroureter), an IVU is useful for assessing the anatomical location of the obstruction. Antegrade or retrograde pyelography will show similar findings to an IVU but offer a therapeutic option as well. Real-time ultrasounds and Doppler ultrasound tests in association with vascular resistance testing helps determine how a given obstruction is effecting urinary functionality in hydronephrotic patients.

In determining the cause of hydronephrosis, it is important to rule out urinary obstruction. One way to do this is to test the kidney function. This can be done by, for instance, a diuretic intravenous pyelogram, in which the urinary system is observed radiographically after administration of a diuretic, such as 5% mannitol, and an intravenous iodine contrast. The location of obstruction can be determined with a Whittaker (or pressure perfusion) test, wherein the collecting system of the kidney is accessed percutaneously, and the liquid is introduced at high pressure and constant rate of 10ml/min while measuring the pressure within the renal pelvis. A rise in pressure above 22 cm HO suggests that the urinary collection system is obstructed. When arriving at this pressure measurement, bladder pressure is subtracted from the initial reading of internal pressure. (The test was first described by Whittaker in 1973 to test the hypothesis that patients' whose hydronephrosis persists after the posterior urethral valves have been ablated usually have ureters that are not obstructed, even though they may be dilated.)

Kay recommends that a neonate born with untreated in utero hydronephrosis receive a renal ultrasound within two days of birth. A renal pelvis greater than 12mm in a neonate is considered abnormal and suggests significant dilation and possible abnormalities such as obstruction or morphological abnormalities in the urinary tract.

The choice of imaging depends on the clinical presentation (history, symptoms and examination findings). In the case of renal colic (one sided loin pain usually accompanied by a trace of blood in the urine) the initial investigation is usually a spiral or helical CT scan. This has the advantage of showing whether there is any obstruction of flow of urine causing hydronephrosis as well as demonstrating the function of the other kidney. Many stones are not visible on plain X-ray or IVU but 99% of stones are visible on CT and therefore CT is becoming a common choice of initial investigation. CT is not used however, when there is a reason to avoid radiation exposure, e.g. in pregnancy.

For incidentally detected prenatal hydronephrosis, the first study to obtain is a postnatal renal ultrasound, since as noted, many cases of prenatal hydronephrosis resolve spontaneously. This is generally done within the first few days after birth, although there is some risk that obtaining an imaging study this early may miss some cases of mild hydronephrosis due to the relative oliguria of a newborn. Thus, some experts recommend obtaining a follow up ultrasound at 4–6 weeks to reduce the false-negative rate of the initial ultrasound. A voiding cystourethrogram (VCUG) is also typically obtained to exclude the possibility of vesicoureteral reflux or anatomical abnormalities such as posterior urethral valves. Finally, if hydronephrosis is significant and obstruction is suspected, such as a ureteropelvic junction (UPJ) or ureterovesical junction (UVJ) obstruction, a nuclear imaging study such as a MAG-3 scan is warranted.

Before the advancement of modern medicine, renal failure was often referred to as uremic poisoning. Uremia was the term for the contamination of the blood with urine. It is the presence of an excessive amount of urea in blood. Starting around 1847, this included reduced urine output, which was thought to be caused by the urine mixing with the blood instead of being voided through the urethra. The term "uremia" is now used for the illness accompanying kidney failure.

In people with microscopic hematuria, it is important to rule out any possible confounders such as menstruation in women, possible presence of semen in sample or recent rigorous exercise. In menstruating women, tests should be repeated during non-bleeding parts of their cycles. In individuals with history of recent rigorous exercise, urinalysis should be repeated 4–6 weeks following cessation of exercise. All women of child-bearing age should undergo a pregnancy test, and if positive should receive an ultrasound of their kidneys and bladder with further invasive diagnostic work-up deferred until completion of pregnancy.

If diagnostic work-up has been unyielding so far or the aforementioned risk factors are present, it is important to begin a thorough work-up for possible malignancy especially of the bladder and kidney by referring to a Urologist to look at the urethra and bladder with a cystoscopy and also performing additional imaging using CT urography, which provides a thorough view of the complete urinary system.

For individuals with persistent hematuria with no immediate identifiable cause, urinalysis should be repeated once a year, and if it is negative for 2 years then you can stop repeating the tests. However, if it is positive for 3 years, repeat anatomic evaluation should be done.

For people with visible hematuria and evidence of blood clots, further imaging with an abdominal CT scan should be done and an urgent referral to a urologist made. Otherwise, the next step involves determining if source of bleeding is glomerular in nature as evidenced by presence of inappropriately shaped/dysmorphic red blood cells, presence of protein in the urine, new or worsening hypertension or swelling. If source is glomerular patients should be referred to a nephrologist for further evaluation. Non-glomerular source of bleeding will usually require further work-up by a urologist.

Jackstone calculi are rare bladder stones that have an appearance resembling toy jacks. They are almost always composed of calcium oxalate dihydrate and consist of a dense central core and radiating . They are typically light brown with dark patches and are usually formed in the urinary bladder and rarely in the upper urinary tract. Their appearance on plain radiographs and computed tomography in human patients is usually easily recognizable. Jackstones often must be removed via cystolithotomy.

The Society of Fetal Ultrasound has developed a grading system for hydronephrosis, initially intended for use in neonatal and infant hydronephrosis, but it is now used for grading hydronephrosis in adults as well:

- Grade 0 – No renal pelvis dilation. This means an anteroposterior diameter of less than 4 mm in fetuses up to 32 weeks of gestational age and 7 mm afterwards. In adults, cutoff values for renal pelvic dilation have been defined differently by different sources, with anteroposterior diameters ranging between 10 and 20 mm. About 13% of normal healthy adults have a transverse pelvic diameter of over 10 mm.

- Grade 1 (mild) – Mild renal pelvis dilation (anteroposterior diameter less than 10 mm in fetuses) without dilation of the calyces nor parenchymal atrophy

- Grade 2 (mild) – Moderate renal pelvis dilation (between 10 and 15 mm in fetuses), including a few calyces

- Grade 3 (moderate) – Renal pelvis dilation with all calyces uniformly dilated. Normal renal parenchyma

- Grade 4 (severe) – As grade 3 but with thinning of the renal parenchyma

Initial treatment is with adequate hydration, alkalization of the urine with citrate supplementation or acetazolamide, and dietary modification to reduce salt and protein intake (especially methionine). If this fails then patients are usually started on chelation therapy with an agent such as penicillamine. Tiopronin is another agent.

Once renal stones have formed, however, the first-line treatment is ESWL (Extracorporeal shock wave lithotripsy). If ESWL do not work efficiently surgery can be necessary. Both endoscopic surgery and conventional open-abdominal surgery have proven to be effective treatment modalities for patients with more advanced disease. Adequate hydration is the foremost aim of treatment to prevent cysteine stones. The goal is to increase the urine volume because the concentration of cystine in the urine is reduced which prevents cystine from precipitating from the urine and forming stones. People with cystine stones should consume 5 to 7 liters a day. The rationale behind alkalizing the urine is that cystine tends to stay in solution and causes no harm. In order to alkalize the urine, sodium biocarbonate has been used. One must be careful in alkalizing their urine because it could lead to other forms of stones in process of preventing cystine stones. Penicillamine is a drug that acts to form a complex with cystine that is 50 times more soluble than cystine itself. Percutaneous nephrolithotripsy (PNL) is performed via a port created by puncturing the kidney through the skin and enlarging the access port to 1 cm in diameter. Most of the time, cystine stones are too dense to be broken up by shock (ESWL) so PNL is needed.

Videos of surgery are available on various websites that show stone removal by percutaneous nephrolithotomy.

In February 2017, an article was published in Nature Medicine entitled 'Alpha lipoic acid treatment prevents cystine urolithiasis in a mouse model of cystinuria', suggesting that a high dose of the readily available antioxidant, alpha-lipoic acid at 2,700 mg/67 kg body weight daily reduced the incidence of stones. The effects were dose dependent. The results are unprecedented for cystinuria. A clinical trial is underway based on this mouse model.

Millions of people across the world suffer from kidney disease. Of those millions, several thousand will eventually or do need kidney transplants. Out of those millions in the world, 16,500 in the United States needed a kidney transplant in 2008. Of those 16,500 people, 5,000 died while waiting for a transplant. Currently, there is a shortage of donors, and in 2007 there were only 64,606 kidney transplants in the world. This shortage of donors is causing countries to place monetary value on kidneys. Countries such as Iran and Singapore are eliminating their lists by paying their citizens to donate. Also, the black market accounts for 5-10 percent of transplants that occur worldwide. The act of buying an organ through the black market is illegal in the United States. To be put on the waiting list for a kidney transplant, patients must first be referred by a physician, then they must choose and contact a donor hospital. Once they choose a donor hospital, patients must then receive an evaluation to make sure they are sustainable to receive a transplant. In order to be a match for a kidney transplant, patients must match blood type and human leukocyte antigen factors with their donors. They must also have no reactions to the antibodies from the donor’s kidneys.

Modification of predisposing factors can sometimes slow or reverse stone formation. Treatment varies by stone type, but, in general:

- Medication

- Surgery (lithotomy)

- Antibiotics and/or surgery for infections

- Medication

- Extracorporeal shock wave lithotripsy (ESWL) for removal of calculi

If a kidney stone is suspected (e.g. on the basis of characteristic colicky pain or the presence of a disproportionate amount of blood in the urine), a kidneys, ureters, and bladder x-ray (KUB film) may assist in identifying radioopaque stones. Where available, a noncontrast helical CT scan with 5 millimeter sections is the diagnostic modality of choice in the radiographic evaluation of suspected nephrolithiasis. All stones are detectable on CT scans except very rare stones composed of certain drug residues in the urine. In patients with recurrent ascending urinary tract infections, it may be necessary to exclude an anatomical abnormality, such as vesicoureteral reflux or polycystic kidney disease. Investigations used in this setting include kidney ultrasonography or voiding cystourethrography. CT scan or kidney ultrasonography is useful in the diagnosis of xanthogranulomatous pyelonephritis; serial imaging may be useful for differentiating this condition from kidney cancer.

Ultrasound findings that indicate pyelonephritis are enlargement of the kidney, edema in the renal sinus or parenchyma, bleeding, loss of corticomedullary differentiation, abscess formation, or an areas of poor blood flow on doppler ultrasound. However, ultrasound findings are seen in only 20% to 24% of people with pyelonephritis.

A DMSA scan is a radionuclide scan that uses dimercaptosuccinic acid in assessing the kidney morphology. It is now the most reliable test for the diagnosis of acute pyelonephritis.

Increase the water intake to prevent oxalates to precipitate .

Minimize dietary intake of oxalates by restricting the intake of leafy vegetables , sesame seeds , tea , cocoa , beet root , spinach , rhubarb , etc.

Treatment is dependent on the underlying cause of this symptom. The most easily treatable cause is obstruction of urine flow, which is often solved by insertion of a urinary catheter into the urinary bladder.

Mannitol is a medicine that is used to increase the amount of water removed from the blood and thus improve the blood flow to the kidneys. However, mannitol is contraindicated in anuria secondary to renal disease, severe dehydration, intracranial bleeding (except during craniotomy), severe pulmonary congestion, or pulmonary edema.

Dextrose and Dobutamine are both used to increase blood flow to the kidney and act within 30 to 60 minutes.

Analysis of the urine may show signs of urinary tract infection. Specifically, the presence of nitrite and white blood cells on a urine test strip in patients with typical symptoms are sufficient for the diagnosis of pyelonephritis, and are an indication for empirical treatment. Blood tests such as a complete blood count may show neutrophilia. Microbiological culture of the urine, with or without blood cultures and antibiotic sensitivity testing are useful for establishing a formal diagnosis, and are considered mandatory.