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.

Urinary catheters should be inserted using aseptic technique and sterile equipment (including sterile gloves, drape, sponges, antiseptic and sterile solution), particularly in an acute care setting. Hands should be washed before and after catheter insertion. Overall, catheter use should be minimized in all patients, particularly those at higher risk of CAUTI and mortality (e.g. the elderly or those with impaired immunity).

IC/BPS has a profound impact on quality of life. A 2007 Finnish epidemiologic study showed that two-thirds of women at moderate to high risk of having interstitial cystitis reported impairment in their quality of life and 35% of IC patients reported an impact on their sexual life. A 2012 survey showed that among a group of adult women with symptoms of interstitial cystitis, 11% reported suicidal thoughts in the past two weeks. Other research has shown that the impact of IC/BPS on quality of life is severe and may be comparable to the quality of life experienced in end-stage kidney disease or rheumatoid arthritis.

International recognition of interstitial cystitis has grown and international urology conferences to address the heterogeneity in diagnostic criteria have recently been held. IC/PBS is now recognized with an official disability code in the United States of America.

Some genetic subtypes, in some people, have been linked to the disorder.

- An antiproliferative factor is secreted by the bladders of people with IC/BPS which inhibits bladder cell proliferation, thus possibly causing the missing bladder lining.

- PAND, at gene map locus 13q22–q32, is associated with a constellation of disorders (a "pleiotropic syndrome") including IC/BPS and other bladder and kidney problems, thyroid diseases, serious headaches/migraines, panic disorder, and mitral valve prolapse.

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.

Bacteria and yeast, including those naturally occurring as part of the human microbiome, can travel along urinary catheters and cause an infection in the bladder, kidneys, and other organs connected to the urinary tract.

CAUTI can lead to complications such as prostatitis, epididymitis, and orchitis in men, and cystitis, pyelonephritis, gram-negative bacteremia, endocarditis, vertebral osteomyelitis, septic arthritis, endophthalmitis, and meningitis in all patients. Complications associated with CAUTI cause discomfort to the patient, prolonged hospital stay, and increased cost and mortality. It has been estimated that more than 13,000 deaths are associated with UTIs annually. Estimated > 560,000 nosocomial UTIs annually.

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.

Treatment involves avoiding the trigger if that can be determined.

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.

The drug Elmiron helps, for some patients, to prevent the formation of Hunner's Ulcers by coating the bladder wall, thus making it harder for the acid in urine to irritate the bladder wall lining, which can lead to ulceration. (not cited)

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.

Risk factors include catheter use and chronic urinary tract infections, being female, diabetes mellitus, neurogenic bladder, and being in an immunocompromised state (Weerakkody). In 50% of cases, patients are elderly and diabetic. Obstruction of the urinary tract as well as urinary stasis, often brought on by paralysis of the urinary tract, are also major risk factors in addition to diabetes (De Baets, Baert). Transplant recipients have also been found to be at risk (Weerakkody). Introduction of infection from external means was discovered in one case study where a male with no history of diabetes or abnormalities to his immune system had recently undergone a transrectal ultrasound needle-guided prostate biopsy contracted a severe case of sepsis, which led to a case of Emphysematous cystitis. The patient went on to develop disseminated intravascular coagulopathy and acute respiratory distress syndrome. After a stay in Intensive Care undergoing broad-spectrum antibiotic therapy, the patient was eventually discharged in stable condition (Hashimoto, Takeshi). Patients diagnosed with Emphysematous Cystitis are also commonly diagnosed with urinary tract infections and sepsis (Mccabe). Cases of Emphysematous Cystitis in a clinical study have shown to progress quickly and are life threatening and sometimes fatal due to inflammation caused by gas forming organisms (Mokabberi).

Bladder rupture (rupture of bladder, ) may occur if the bladder is overfilled and not emptied. This can occur in the case of binge drinkers who have consumed large quantities of fluids, but are not conscious of the need to urinate due to stupor. This condition is very rare in women, but does occur. Signs and symptoms include localized pain and uraemia (poisoning due to reabsorbed waste).

Eosinophilic cystitis is a rare condition where eosinophiles are present in the bladder wall. Signs and symptoms are similar to a bladder infection. Its cause is not entirely clear; however, may be linked to food allergies, infections, and medications among others.

Glomerulation refers to bladder hemorrhages which are thought to be associated with some types of interstitial cystitis (IC).

The presence of glomerulations, also known as petechial hemorrhages, in the bladder suggests that the bladder wall has been damaged, irritated and/or inflamed. In fact, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Diagnostic Criteria for IC, developed in 1987, required the presence of glomerulations or Hunner's Ulcers to make a firm diagnosis of IC and is still used, today, to determine patient eligibility for some clinical trials. Research conducted by Waxman, however, determined that the hydrodistention procedure itself may have created these tiny broken blood vessels. Thus, a diagnosis of IC is now based upon other, less invasive methods, such as the PUF questionnaire.

In addition to traditional IC therapies, diet modification remains a core self care strategy as foods that are irritating to the bladder dramatically worsen the symptoms that patients may experience. Foods high in acid and/or caffeine (such as all coffees, regular teas, green teas, sodas, diet sodas, artificial sweeteners and most fruit juices) should be avoided. The daily goal of patients should be to soothe rather than irritate the bladder wall.

In a small minority of cases of urethral syndrome, treatment with antibiotics is effective, which indicates that in some cases it may be caused by bacterial infection which does not show up in either urinalysis or urine culture. For chronic urethral syndrome, a long term, low-dose antibiotic treatment is given on a continuous basis or after intercourse each time if intercourse appears to trigger symptoms.

As low oestrogen may also be considered a source for urethral syndrome, hormone replacement therapy, and oral contraceptive pill (birth-control pills) containing oestrogen are also used to treat the symptoms of this condition in women.

Cystitis glandularis is a term describing a metaplasial transformation of mucosal cells lining the urinary bladder. The main importance is in histopathology, distinguishing the metaplastic change from urothelial cell carcinoma. It is a very common finding in bladder biopsies and cystectomies, and most often found in the trigone area. Cystitis glandularis lesions are usually present as small microscopic foci; however, occasionally it can form raised intramucosal or polypoid lesions. The cystitis glandularis lesions are within the submucosa.

The symptoms of CP/CPPS appear to result from an interplay between psychological factors and dysfunction in the immune, neurological, and endocrine systems.

Theories behind the disease include stress-driven hypothalamic-pituitary-adrenal axis dysfunction and adrenocortical hormone (endocrine) abnormalities, neurogenic inflammation, and myofascial pain syndrome. In the latter two categories, dysregulation of the local nervous system due to past trauma, infection or an anxious disposition and chronic albeit unconscious pelvic tensing lead to inflammation that is mediated by substances released by nerve cells (such as substance P). The prostate (and other areas of the genitourinary tract: bladder, urethra, testicles) can become inflamed by the action of the chronically activated pelvic nerves on the mast cells at the end of the nerve pathways. Similar stress-induced genitourinary inflammation has been shown experimentally in other mammals. However, there is no correlation between inflammation on histological examination of the prostate and the National Institutes of Health Chronic Prostatitis Symptom Index.

The bacterial infection theory that for so long had held sway in this field was shown to be unimportant in a 2003 study from the University of Washington team led by Dr Lee and Professor Richard Berger. The study found that one third of both normal men and patients had equal counts of similar bacteria colonizing their prostates. This view was endorsed by Dr Anthony Schaeffer, Professor and Chairman of the Department of Urology at Northwestern University, in a 2003 editorial of "The Journal of Urology", in which he stated that ""...these data suggest that bacteria do not have a significant role in the development of the chronic pelvic pain syndrome"", and a year later with his colleagues he published studies showing that antibiotics are essentially useless for CP/CPPS. Since the publication of these studies, the research focus has shifted from infection to neuromuscular, behavioral, psychological, and genetic cause for UCPPS (CP/CPPS and IC/PBS), where the interplay between the lower urinary tract and other physiological systems is stressed. UCPPS is now studied as a systemic disorder. In support of this approach, a 2005 study showed that stress is correlated to Cat III prostatitis.

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.

The ambient temperature appears to play a role as cold is frequently reported as causing symptom aggravation and heat is often reported to be ameliorating. It appears that cold is one of the factors that can trigger a process resulting in CP/CPPS. Cold also causes aggravation of symptoms and can initiate a relapse. A survey showed that the occurrence of prostatitis symptoms in men living in northern Finland —a cold climate—is higher than that reported in other parts of the world. This could be partly caused by the cold climate.

Most cases of "community-acquired" pyelonephritis are due to bowel organisms that enter the urinary tract. Common organisms are "E. coli" (70–80%) and "Enterococcus faecalis". Hospital-acquired infections may be due to coliform bacteria and enterococci, as well as other organisms uncommon in the community (e.g., "Pseudomonas aeruginosa" and various species of "Klebsiella"). Most cases of pyelonephritis start off as lower urinary tract infections, mainly cystitis and prostatitis. "E. coli" can invade the superficial umbrella cells of the bladder to form intracellular bacterial communities (IBCs), which can mature into biofilms. These biofilm-producing "E. coli" are resistant to antibiotic therapy and immune system responses, and present a possible explanation for recurrent urinary tract infections, including pyelonephritis. Risk is increased in the following situations:

- Mechanical: any structural abnormalities in the urinary tract, vesicoureteral reflux (urine from the bladder flowing back into the ureter), kidney stones, urinary tract catheterization, ureteral stents or drainage procedures (e.g., nephrostomy), pregnancy, neurogenic bladder (e.g., due to spinal cord damage, spina bifida or multiple sclerosis) and prostate disease (e.g., benign prostatic hyperplasia) in men

- Constitutional: diabetes mellitus, immunocompromised states

- Behavioral: change in sexual partner within the last year, spermicide use

- Positive family history (close family members with frequent urinary tract infections)

There are two main types of cystitis glandularis, non-mucinous and mucinous (intestinal). The difference is in the cellular production of mucin, a normal feature of colonic and intestinal epithelial cells but not of urothelial cells. Another distinction is made between focal areas and diffuse involvement of the bladder. Whereas focal areas are more common, diffuse involvement is seen in chronically irritated bladders, such as in paraplegics or those with bladder stones or indwelling catheters. Individuals with diffuse intestinal-type cystitis glandularis are at increased risk for developing bladder cancer.

Signs and symptoms of emphysematous cystitis include air in the bladder wall, altered mental status, severe abdominal pain, weakness, dark urine, dysuria, fever, lethargy, vomiting, as well as white blood cells and bacteria in the urine (Mccabe). Where some patients may be asymptomatic, others may present with septic shock (De Baets, Baert). Symptoms can vary greatly from patient to patient, which makes the disease difficult to diagnose. In some cases of emphysematous cystitis, patients do not even claim to have any urinary symptoms (Mokabberi). Urinary symptoms can include blood in the urine, increased urinary frequency, urgency, occasional incontinence, difficulty voiding, and burning sensation. Emphysematous cystitis is often indicated in patients who have air in the urine (Bobba). In some cases, emphysematous cystitis can cause thickening of the bladder wall (Weerakkody). Clinical subcutaneous emphysema is a rare complication of emphysematous cystitis that has a poor prognosis (Ahmed-Ramadan, Blake).