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.

Renal failure is defined by functional impairment of the kidney. Renal failure can be acute or chronic, and can be further broken down into categories of pre-renal, intrinsic renal and post-renal.

Pre-renal failure refers to impairment of supply of blood to the functional nephrons including renal artery stenosis. Intrinsic renal diseases are the classic diseases of the kidney including drug toxicity and nephritis. Post-renal failure is outlet obstruction after the kidney, such as a kidney stone or prostatic bladder outlet obstruction.

Renal failure may require medication, dietary and lifestyle modification and dialysis.

Primary renal cell carcinomas as well as metastatic cancers can affect the kidney.

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.

Duplicated ureter is the most common renal abnormality, occurring in approximately 1% of the population.

Race: Duplicated ureter is more common in Caucasians than in African-Americans.

Sex: Duplicated ureter is more common in females. However, this may be due to the higher frequency of urinary tract infections in females, leading to a higher rate of diagnosis of duplicated ureter.

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.

Complications of analgesic nephropathy include pyelonephritis and end-stage kidney disease. Risk factors for poor prognosis include recurrent urinary tract infection and persistently elevated blood pressure. Analgesic nephropathy also appears to increase the risk of developing cancers of the urinary system.

Patients with ESKD are at increased overall risk for cancer. This risk is particularly high in younger patients and gradually diminishes with age. Medical specialty professional organizations recommend that physicians do not perform routine cancer screening in patients with limited life expectancies due to ESKD because evidence does not show that such tests lead to improved patient outcomes.

The prognosis of nephrocalcinosis is determined by the underlying cause. Most cases of nephrocalcinosis do not progress to end stage renal disease, however if not reated it can lead to renal dysfunction this includes primary hyperoxaluria, hypomagnesemic hypercalciuric nephrocalcinosis and Dent's disease. Once nephrocalcinosis is found, it is unlikely to be reversed, however, partial reversal has been reported in patients who have had successful treatment of hypercalciuria and hyperoxaluria following corrective intestinal surgery.

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.

Male gender, proteinuria (especially > 2 g/day), hypertension, smoking, hyperlipidemia, older age, familial disease and elevated creatinine concentrations are markers of a poor outcome. Frank hematuria has shown discordant results with most studies showing a better prognosis, perhaps related to the early diagnosis, except for one group which reported a poorer prognosis. Proteinuria and hypertension are the most powerful prognostic factors in this group.

There are certain other features on kidney biopsy such as interstitial scarring which are associated with a poor prognosis. ACE gene polymorphism has been recently shown to have an impact with the DD genotype associated more commonly with progression to kidney failure.

In ADPKD patients, gradual cyst development and expansion result in kidney enlargement, and during the course of the disease, glomerular filtration rate (GFR) remains normal for decades before kidney function starts to progressively deteriorate, making early prediction of renal outcome difficult. The CRISP study, mentioned in the treatment section above, contributed to build a strong rationale supporting the prognostic value of total kidney volume (TKV) in ADPKD; TKV (evaluated by MRI) increases steadily and a higher rate of kidney enlargement correlated with accelerated decline of GFR, while patient height-adjusted TKV (HtTKV) ≥600 ml/m predicts the development of stage 3 chronic kidney disease within 8 years.

Besides TKV and HtTKV, the estimated glomerular filtration rate (eGFR) has also been tentatively used to predict the progression of ADPKD. After the analysis of CT or MRI scans of 590 patients with ADPKD treated at the Mayo Translational Polycystic Kidney Disease Center, Irazabal and colleagues developed an imaging-based classification system to predict the rate of eGFR decline in patients with ADPKD. In this prognostic method, patients are divided into five subclasses of estimated kidney growth rates according to age-specific HtTKV ranges (1A, 6.0%) as delineated in the CRISP study. The decline in eGFR over the years following initial TKV measurement is significantly different between all five patient subclasses, with those in subclass 1E having the most rapid decline.

According to the United States Renal Data System (USRDS), hypertensive nephropathy accounts for more than one-third of patients on hemodialysis and the annual mortality rate for patients on hemodialysis is 23.3%.

Haemodialysis is recommended for patients who progress to end-stage kidney disease (ESKD) and hypertensive nephropathy is the second most common cause of ESKD after diabetes.

Patient prognosis is dependent on numerous factors including age, ethnicity, blood pressure and glomerular filtration rate. Changes in lifestyle factors, such as reduced salt intake and increased physical activity have been shown to improve outcomes but are insufficient without pharmacological treatment.

Renal tuberculosis

And other causes of hypercalcemia (and thus hypercalciuria)

- Immobilization (leading to hypercalcemia and hypercalciuria)

- Milk-alkali syndrome

- Hypervitaminosis D

- Multiple myeloma

There are roughly 12–13 cases annually per 10,000 population in women receiving outpatient treatment and 3–4 cases requiring admission. In men, 2–3 cases per 10,000 are treated as outpatients and 1– cases/10,000 require admission. Young women are most often affected, probably reflecting sexual activity in that age group. Infants and the elderly are also at increased risk, reflecting anatomical changes and hormonal status. Xanthogranulomatous pyelonephritis is most common in middle-aged women. It can present somewhat differently in children, in whom it may be mistaken for Wilms' tumor.

Duplicated ureter or Duplex Collecting System is a congenital condition in which the ureteric bud, the embryological origin of the ureter, splits (or arises twice), resulting in two ureters draining a single kidney. It is the most common renal abnormality, occurring in approximately 1% of the population. The additional ureter may result in a ureterocele, or an ectopic ureter.

CKD increases the risk of cardiovascular disease, and people with CKD often have other risk factors for heart disease, such as high blood lipids. The most common cause of death in people with CKD is cardiovascular disease rather than kidney failure.

Chronic kidney disease results in worse all-cause mortality (the overall death rate) which increases as kidney function decreases. The leading cause of death in chronic kidney disease is cardiovascular disease, regardless of whether there is progression to stage 5.

While renal replacement therapies can maintain people indefinitely and prolong life, the quality of life is negatively affected. Kidney transplantation increases the survival of people with stage 5 CKD when compared to other options; however, it is associated with an increased short-term mortality due to complications of the surgery. Transplantation aside, high-intensity home hemodialysis appears to be associated with improved survival and a greater quality of life, when compared to the conventional three-times-a-week hemodialysis and peritoneal dialysis.

Hemorrhagic cystitis or Haemorrhagic cystitis is defined by lower urinary tract symptoms that include dysuria, hematuria, and hemorrhage. The disease can occur as a complication of cyclophosphamide, ifosfamide and radiation therapy. In addition to hemorrhagic cystitis, temporary hematuria can also be seen in bladder infection or in children as a result of viral infection.

Common findings in people with analgesic nephropathy include headache, anemia, high blood pressure (hypertension), and white blood cells in the urine (pyuria). Some individuals with analgesic nephropathy may also have protein in their urine (proteinuria).

Treatment of renal papillary necrosis is supportive, any obstruction (urethral) can be dealt with via stenting. This condition is not linked to a higher possibility of renal failure. Control of infection is important, thus antimicrobial treatment is begun, so as to avert surgery (should the infection not respond).

The pathophysiology of this condition can be due to analgesic nephropathy, which in turn is a result of long-term use of aspirin. It is a sequence of vascular occlusion, vasospasm, then infection and finally obstruction which leads to RPN.

It is accepted that kidney transplantation is the preferred treatment for ADPKD patients with end-stage renal disease (ESRD). Among American patients on the kidney transplant waiting list (as of December 2011), 7256 (8.4%) were listed due to cystic kidney disease and of the 16,055 renal transplants performed in 2011, 2057 (12.8%) were done for patients with cystic kidney disease, with 1,189 from deceased donors and 868 from living donors.

In regard to the epidemiology of multicystic dysplasia kidney, the incidence of MCDK is estimated to be 1 in every 4,000 live births, making it rare in terms of the general population.

In one review, over half of individuals with shunt nephritis made a complete recovery. An additional 40% of individuals had persistent urine abnormalities or end-stage renal disease. Death occurred in 9%.

Up to 27 percent of individuals greater than 50 years of age may have simple renal cysts that cause no symptoms.

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.