It has been estimated that VUR is present in more than 10% of the population. Younger children are more prone to VUR because of the relative shortness of the submucosal ureters. This susceptibility decreases with age as the length of the ureters increases as the children grow. In children under the age of 1 year with a urinary tract infection, 70% will have VUR. This number decreases to 15% by the age of 12. Although VUR is more common in males antenatally, in later life there is a definite female preponderance with 85% of cases being female.

The American Urological Association recommends ongoing monitoring of children with VUR until the abnormality resolves or is no longer clinically significant. The recommendations are for annual evaluation of blood pressure, height, weight, analysis of the urine, and kidney ultrasound.

If left untreated, complications may arise including abscess formation, peritonitis, sepsis, and damage to the urinary tract by fibrosis and granuloma formation. It is recommended, as a first step, to drain the lesion with ultrasound or CT guidance. If a patient has an underlying obstructive problem it needs to be addressed according to its cause.

A common cause of pneumaturia is colovesical fistula (communication between the colon and bladder). These may occur as a complication of diverticular disease.

Other key differentials:

- Crohn's disease

- Carcinoma of the colon or bladder

- A gas-producing UTI (emphysematous cystitis: rare).

Male scuba divers utilizing condom catheters or female divers using a She-p external catching device for their dry suits are also susceptible to pneumaturia.

A urinoma, also pararenal pseudocyst, is an encapsulated collection of extravasated urine and typically found in the area adjacent to the kidneys or to extend into the retroperitoneum.

Urinothorax ("pl". urinothoraces) means urine in the fluid-filled cavity that surrounds the lungs. It is a rare cause of pleural effusion secondary to obstructive uropathy whereby urine forms a collection in the pleural cavity. The urine arrives in the pleural space either retroperitoneally under the posterior diaphragm, or via the retroperitoneal lymphatics. It remains a rare, possibly under-diagnosed, differential in the case of transudative pleural effusion.

Handa et al., described 47 cases between 1967 and 2007, noting that it was more prevalent in males, generally ipsilateral to the obstruction, and in most cases relieved by clearance of the obstruction.

Bladder stones may occur whenever the kidneys, bladder, or ureters become inflamed, which may occur when the urine becomes too concentrated or when the body becomes dehydrated. Minerals such as calcium and magnesium crystallize into the stones, which then can cause such symptoms as lower back or abdominal pain or difficulty with urination. The use of urinary catheters may cause a bladder stone. Individuals who are paralyzed or are unable to adequately pass urine may require the use of small plastic tubes (catheters) placed into the bladder. The use of these tubes may lead to an infection, which irritates the bladder, resulting in stone formation. Finally, a kidney stone may travel down the ureter into the bladder and become a bladder stone. There is some evidence indicating that chronic irritation of the bladder by retained stones may increase the chance of bladder cancer. Urinary schistosomiasis, a disease caused by the digenean trematode "Schistosoma haematobium", has been implicated in the development of vesical calculi. However, evidence accumulated thus far has not supported this hypothesis.

Urinary stones may be composed of the following substances:

- Calcium oxalate monohydrate (whewellite)

- Calcium oxalate dihydrate (weddellite)

- Calcium phosphate

- Magnesium phosphate

- Ammonium phosphate

- Ammonium magnesium phosphate (struvite)

- Calcium hydroxyphosphate (apatite)

- Uric acid and its salts (urates)

- Cystine

- Xanthine

- Indigotin (rare)

- Urostealith (rare)

- Sulfonamide (rare)

The evidence linking vitamin C supplements with an increased rate of kidney stones is inconclusive. The excess dietary intake of vitamin C might increase the risk of calcium oxalate stone formation, in practice this is rarely encountered. The link between vitamin D intake and kidney stones is also tenuous. Excessive vitamin D supplementation may increase the risk of stone formation by increasing the intestinal absorption of calcium; correction of a deficiency does not.

Diagnosis is made by patient history of passing air or a sputtering urine stream. CT scans may show air in the urinary bladder or bladder walls.

Diets in Western nations typically contain a large proportion of animal protein. Consumption of animal protein creates an acid load that increases urinary excretion of calcium and uric acid and reduced citrate. Urinary excretion of excess sulfurous amino acids (e.g., cysteine and methionine), uric acid, and other acidic metabolites from animal protein acidifies the urine, which promotes the formation of kidney stones. Low urinary citrate excretion is also commonly found in those with a high dietary intake of animal protein, whereas vegetarians tend to have higher levels of citrate excretion. Low urinary citrate, too, promotes stone formation.

Tobacco smoking is associated with an increased risk of ureteral cancer.

The causes of diseases of the body are common to the urinary tract. Structural and or traumatic change can lead to hemorrhage, functional blockage or inflammation. Colonisation by bacteria, protozoa or fungi can cause infection. Uncontrolled cell growth can cause neoplasia.

For example:

- Urinary tract infections (UTIs), interstitial cystitis

- incontinence (involuntary loss of urine), benign prostatic hyperplasia (where the prostate overgrows), prostatitis (inflammation of the prostate).

- Urinary retention, which is a common complication of benign prostatic hyperplasia (BPH), though it can also be caused by other types of urinary tract obstruction, nerve dysfunction, tethered spinal cord syndrome, constipation, infection and certain medications.

- Transitional cell carcinoma (bladder cancer), renal cell carcinoma (kidney cancer), and prostate cancer are examples of neoplasms affecting the urinary system.

- Urinary tract obstruction

The term "uropathy" refers to a disease of the urinary tract, while "nephropathy" refers to a disease of the kidney.

Extravasation of urine due to blunt renal trauma or ureteral obstruction can lead to the formation of an urinoma.

Greater than 50% of cases of visible hematuria in children have an identifiable cause. Common causes of visible hematuria in pediatric populations are:

- urinary tract infection

- perineal or urethral irritation

- congenital abnormalities–

- Non-vascular—ureteropelvic junction obstruction, posterior urethral valves, urethral prolapse, urethral diverticula, multicystic dysplastic kidney

- Vascular—arteriovenous malformations, hereditary hemorrhagic telangiectasias, renal vascular thromboses

- trauma

- acute nephritis—characterized by visible hematuria, white blood cells in the urine, and a transient decline in renal function, commonly caused by medications

- coagulopathy

- kidney stones

- IgA nephropathy–suspected in a child with dark urine and recent upper respiratory infection

- Post-streptococcal glomerulonephritis–suspected in a child with dark brown urine following recent streptoccocal pharyngitis or impetigo

Rupture of the urethra is an uncommon result of penile injury, incorrect catheter insertion, straddle injury, or pelvic girdle fracture. The urethra, the muscular tube that allows for urination, may be damaged by trauma. When urethral rupture occurs, urine may extravasate (escape) into the surrounding tissues. The membranous urethra is most likely to be injured in pelvic fractures, allowing urine and blood to enter the deep perineal space and subperitoneal spaces via the genital hiatus. The spongy urethra is most likely to be injured with a catheter or in a straddle injury, allowing urine and blood to escape into the scrotum, the penis, and the superficial peritoneal space. Urethral rupture may be diagnosed with a cystourethrogram. Due to the tight adherence of the fascia lata, urine from a urethral rupture cannot spread into the thighs.

There are two types of prostatic stent: temporary and permanent.

Although a permanent prostatic stent is not a medical treatment, it falls under the classification of a surgical procedure. Placement of a permanent prostatic stent is carried out as an outpatient treatment under local, topical or spinal anesthesia and usually takes about 15–30 minutes.

A temporary prostatic stent can be inserted in a similar manner to a Foley catheter, requiring only topical anesthesia.

Asymptomatic bacteriuria is bacteriuria without accompanying symptoms of a urinary tract infection. It is more common in women, in the elderly, in residents of long-term care facilities, and in people with diabetes, bladder catheters and spinal cord injuries. People with a long-term Foley catheter uniformly show bacteriuria. Chronic asymptomatic bacteriuria without urinary tract infection symptoms occurs in as many as 50% of the population in long-term care.

In pregnant women bacteriuria is associated with low birth weight, preterm delivery, and infection of the newborn. Bacteriuria in pregnancy also increase the risk of preeclampsia.

Permanent stents are often metal coils, which are inserted into the male urethra. The braided mesh is designed to expand radially, applying constant gentle pressure to hold open the sections of the urethra that obstruct the flow of urine. The open, diamond-shape cell design of the stent allows the stent to eventually become embedded in the urethra, thus minimizing the risk for encrustation and migration. Permanent stents are used to relieve urinary obstructions secondary to benign prostatic hyperplasia (BPH), recurrent bulbar urethral stricture (RBUS), or detrusor external sphincter dyssynergia (DESD). The main motive for removal of permanent stents is worsening of symptoms even with device fitted. Other reasons have been migration, clot retention, hematuria, and urinary retention. The only FDA approved permanent stent is the Urolume. Usually, permanent stents are used only for men who are unwilling or unable to take medications or who are reluctant or unable to have surgery. Most doctors do not consider permanent stents a viable long-term treatment for most men.

The most worrisome cause of painless, visible blood in the urine is kidney or bladder cancer, especially in a person wth risk factors such as male sex, age over 35, history of smoking, chronic bladder inflammation, and occupational exposures (to aromatic amines and aniline dyes) Between 80-90% of people with bladder cancer initially presented with visible hematuria.

Other causes include

- Exercise-induced hematuria–occurs in up to 30% of long distance runners and often resolves a few days after running cessation

Globally, up to 35% of the population over the age of 60 years is estimated to be incontinent.

In 2014, urinary leakage affected between 30% and 40% of people over 65 years of age living in their own homes or apartments in the U.S. Twenty-four percent of older adults in the U.S. have moderate or severe urinary incontinence that should be treated medically.

Bladder control problems have been found to be associated with higher incidence of many other health problems such as obesity and diabetes. Difficulty with bladder control results in higher rates of depression and limited activity levels.

Incontinence is expensive both to individuals in the form of bladder control products and to the health care system and nursing home industry. Injury related to incontinence is a leading cause of admission to assisted living and nursing care facilities. More than 50% of nursing facility admissions are related to incontinence.

Failure of kidney function, which can have multiple causes including medications or toxins (e.g., antifreeze, cephalosporins, ACEIs); diabetes; high blood pressure. Stones or tumours in the urinary tract can also cause it by creating an obstruction to urinary flow. High blood calcium, oxalate, or uric acid, can contribute to the risk of stone formation. In males, an enlarged prostate gland is a common cause of obstructive anuria.

Acute anuria, where the decline in urine production occurs quickly, is usually a sign of obstruction or acute renal failure. Acute renal failure can be caused by factors not related to the kidney, such as heart failure, mercury poisoning, infection, and other conditions that cause the kidney to be deprived of blood flow.

Urologic disease can involve congenital or acquired dysfunction of the urinary system.

Kidney diseases are normally investigated and treated by nephrologists, while the specialty of urology deals with problems in the other organs. Gynecologists may deal with problems of incontinence in women.

Diseases of other bodily systems also have a direct effect on urogenital function. For instance, it has been shown that protein released by the kidneys in diabetes mellitus sensitises the kidney to the damaging effects of hypertension.

Diabetes also can have a direct effect on urination due to peripheral neuropathies which occur in some individuals with poorly controlled diabetics.

Anuria itself is a symptom, not a disease. It is often associated with other symptoms of kidney failure, such as lack of appetite, weakness, nausea and vomiting. These are mostly the result of buildup of toxins in the blood which would normally be removed by healthy kidneys.

Extravasation of urine refers to the condition where an interruption of the urethra leads to a collection of urine in other cavities, such as the scrotum or the penis in males. It can be associated with a calculus.