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.

Calcium is one component of the most common type of human kidney stones, calcium oxalate. Some studies suggest people who take calcium or vitamin D as a dietary supplement have a higher risk of developing kidney stones. In the United States, kidney stone formation was used as an indicator of excess calcium intake by the Reference Daily Intake committee for calcium in adults.

In the early 1990s, a study conducted for the Women's Health Initiative in the US found that postmenopausal women who consumed 1000 mg of supplemental calcium and 400 international units of vitamin D per day for seven years had a 17% higher risk of developing kidney stones than subjects taking a placebo. The Nurses' Health Study also showed an association between supplemental calcium intake and kidney stone formation.

Unlike supplemental calcium, high intakes of dietary calcium do not appear to cause kidney stones and may actually protect against their development. This is perhaps related to the role of calcium in binding ingested oxalate in the gastrointestinal tract. As the amount of calcium intake decreases, the amount of oxalate available for absorption into the bloodstream increases; this oxalate is then excreted in greater amounts into the urine by the kidneys. In the urine, oxalate is a very strong promoter of calcium oxalate precipitation—about 15 times stronger than calcium.

A 2004 study found that diets low in calcium are associated with a higher overall risk for kidney stone formation. For most individuals, other risk factors for kidney stones, such as high intakes of dietary oxalates and low fluid intake, play a greater role than calcium intake.

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)

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.

In kidney stones, calcium oxalate is the most common mineral type (see Nephrolithiasis). Uric acid is the second most common mineral type, but an "in vitro" study showed uric acid stones and crystals can promote the formation of calcium oxalate stones.

Stones can cause disease by several mechanisms:

- Irritation of nearby tissues, causing pain, swelling, and inflammation

- Obstruction of an opening or duct, interfering with normal flow and disrupting the function of the organ in question

- Predisposition to infection (often due to disruption of normal flow)

A number of important medical conditions are caused by stones:

- Nephrolithiasis (kidney stones)

- Can cause hydronephrosis (swollen kidneys) and renal failure

- Can predispose to pyelonephritis (kidney infections)

- Can progress to urolithiasis

- Urolithiasis (urinary bladder stones)

- Can progress to bladder outlet obstruction

- Cholelithiasis (gallstones)

- Can predispose to cholecystitis (gall bladder infections) and ascending cholangitis (biliary tree infection)

- Can progress to choledocholithiasis (gallstones in the bile duct) and gallstone pancreatitis (inflammation of the pancreas)

- Gastric calculi can cause colic, obstruction, torsion, and necrosis.

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.

Bladder tamponade is obstruction of the bladder outlet due to heavy blood clot formation within it. It generally requires surgery. Such heavy bleeding is usually due to bladder cancer.

The prognosis of hydronephrosis is extremely variable, and depends on the condition leading to hydronephrosis, whether one (unilateral) or both (bilateral) kidneys are affected, the pre-existing kidney function, the duration of hydronephrosis (acute or chronic), and whether hydronephrosis occurred in developing or mature kidneys.

For example, unilateral hydronephrosis caused by an obstructing stone will likely resolve when the stone passes, and the likelihood of recovery is excellent. Alternately, severe bilateral prenatal hydronephrosis (such as occurs with posterior urethral valves) will likely carry a poor long-term prognosis, because obstruction while the kidneys are developing causes permanent kidney damage even if the obstruction is relieved postnatally.

Hydronephrosis can be a cause of pyonephrosis - which is a urological emergency.

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.

Cystitis is a urinary bladder inflammation that results from any one of a number of distinct syndromes. It is most commonly caused by a bacterial infection in which case it is referred to as a urinary tract infection.

Hydronephrosis is the result of any of several abnormal pathophysiological occurrences. Structural abnormalities of the junctions between the kidney, ureter, and bladder that lead to hydronephrosis can occur during fetal development. Some of these congenital defects have been identified as inherited conditions, however the benefits of linking genetic testing to early diagnosis have not been determined. Other structural abnormalities could be caused by injury, surgery, or radiation therapy.

Compression of one or both ureters can also be caused by other developmental defects not completely occurring during the fetal stage such as an abnormally placed vein, artery, or tumor. Bilateral compression of the ureters can occur during pregnancy due to enlargement of the uterus. Changes in hormone levels during this time may also affect the muscle contractions of the bladder, further complicating this condition.

Sources of obstruction that can arise from other various causes include kidney stones, blood clots, or retroperitoneal fibrosis.

The obstruction may be either partial or complete and can occur anywhere from the urethral meatus to the calyces of the renal pelvis. Hydronephrosis can also result from the reverse flow of urine from the bladder back into the kidneys. This reflux can be caused by some of the factors listed above as well as compression of the bladder outlet into the urethra by prostatic enlargement or impaction of feces in the colon, as well as abnormal contractions of bladder muscles resulting from neurological dysfunction or other muscular disorders.

The incidence of urethral diverticulum has been increasing in the 2000s, likely due to increasing diagnosis and detection of the condition. It is estimated to be present in as low as 0.02% of all women and as high as 6% of all women, and 40% of women with lower urinary tract symptoms. Most symptomatic urethral diverticula are present in women from 30–60 years old.

84% of periurethral masses are due to urethral diverticula.

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.

Urethral diverticulum can occur in men, and can cause complications including kidney stones and urinary tract infections.

Urinary catheterization increases the risk for urinary tract infections. The risk of bacteriuria (bacteria in the urine) is between three and six percent per day and prophylactic antibiotics are not effective in decreasing symptomatic infections. The risk of an associated infection can be decreased by catheterizing only when necessary, using aseptic technique for insertion, and maintaining unobstructed closed drainage of the catheter.

Male scuba divers utilizing condom catheters and female divers utilizing external catching devices for their dry suits are also susceptible to urinary tract infections.

In young sexually active women, sexual activity is the cause of 75–90% of bladder infections, with the risk of infection related to the frequency of sex. The term "honeymoon cystitis" has been applied to this phenomenon of frequent UTIs during early marriage. In post-menopausal women, sexual activity does not affect the risk of developing a UTI. Spermicide use, independent of sexual frequency, increases the risk of UTIs. Diaphragm use is also associated. Condom use without spermicide or use of birth control pills does not increase the risk of uncomplicated urinary tract infection.

Women are more prone to UTIs than men because, in females, the urethra is much shorter and closer to the anus. As a woman's estrogen levels decrease with menopause, her risk of urinary tract infections increases due to the loss of protective vaginal flora. Additionally, vaginal atrophy that can sometimes occur after menopause is associated with recurrent urinary tract infections.

Chronic prostatitis in the forms of chronic prostatitis/chronic pelvic pain syndrome and chronic bacterial prostatitis (not acute bacterial prostatitis or asymptomatic inflammatory prostatitis) may cause recurrent urinary tract infections in males. Risk of infections increases as males age. While bacteria is commonly present in the urine of older males this does not appear to affect the risk of urinary tract infections.

Ectopic ureter (or ureteral ectopia) is a medical condition where the ureter, rather than terminating at the urinary bladder, terminates at a different site. In males this site is usually the urethra, in females this is usually the urethra or vagina. It can be associated with renal dysplasia, frequent urinary tract infections, and urinary incontinence (usually continuous drip incontinence). Ectopic ureters are found in 1 of every 2000–4000 patients, and can be difficult to diagnose, but are most often seen on CT scans.

Ectopic ureter is commonly a result of a duplicated renal collecting system, a duplex kidney with 2 ureters. In this case, usually one ureter drains correctly to the bladder, with the duplicated ureter presenting as ectopic.

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.

Causes of hemorrhagic cystitis include chemotherapy (e.g. cyclophosphamide, Ifosfamide), radiation, or infection. Ifosfamide is the most common cause of hemorrhagic cystitis. Radiation-induced hemorrhagic cystitis develops in similar or smaller patient numbers when compared to cyclophosphamide-induced cases.

Adenovirus (particularly serotypes 11 and 21 of subgroup B) is the most common cause of acute viral hemorrhagic cystitis in children, though it can result from BK virus as well. A chemical hemorrhagic cystitis can develop when vaginal products are inadvertently placed in the urethra. Gentian violet douching to treat candidiasis has resulted in hemorrhagic cystitis when the drug was misplaced in the urethra, but this hemorrhagic cystitis resolved spontaneously with cessation of treatment. Accidental urethral placement of contraceptive suppositories has also caused hemorrhagic cystitis in several patients. The bladder irritation was thought to be caused by the spermicidal detergent nonoxynol-9. In the acute setting, the bladder can be copiously irrigated with alkalinized normal saline to minimize bladder irritation.

Although hemorrhagic cystitis post-transplantation/bone marrow transplantation is not technically infectious, a short discussion is in order for completeness. Patients undergoing therapy to suppress the immune system are at risk for hemorrhagic cystitis due to either the direct effects of chemotherapy or activation of dormant viruses in the kidney, ureter, or bladder.

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.

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

Definitive causes of ureterocele have not been found. While the abnormal growth occurs within the uterus, it has not been substantiated that genetics are to blame.

Many other complications arise from ureteroceles. Redundant collection systems are usually smaller in diameter than single, and predispose the patient to impassable kidney stones. The effective "bladder within a bladder" compounds this problem by increasing the collision of uric acid particles, the process by which uric acid stones are formed. Ureterocele is also associated with poor kidney function. It can cause frequent blockage of the ureter leading to serious kidney damage. In other cases, a small, upper portion of the kidney is congenitally non-functional. Though often benign, this problem can necessitate the removal of non-functioning parts.