Urethroplasty refers to any open reconstruction of the urethra. Success rates range from 85% to 95% and depend on a variety of clinical factors, such as stricture as the cause, length, location, and caliber. Urethroplasty can be performed safely on men of all ages.

In the posterior urethra, anastomotic urethroplasty (with or without preservation of bulbar arteries) is typically performed after removing scar tissue.

In the bulbar urethra, the most common types of urethroplasty are anastomotic (with or without preservation of corpus spongiosum and bulbar arteries) and substitution with buccal mucosa graft, full-thickness skin graft, or split thickness skin graft. These are nearly always done in a single setting (or stage).

In the penile urethra, anastomotic urethroplasties are rare because they can lead to chordee (penile curvature due to a shortened urethra). Instead, most penile urethroplasties are substitution procedures utilizing buccal mucosa graft, full-thickness skin graft, or split thickness skin graft. These can be done in one or more setting, depending on stricture location, severity, cause and patient or surgeon preference.

In boys, history and physical exam is adequate to make the diagnosis. In girls, VCUG (voiding cystourethrogram) is usually diagnostic. Other tests may include:

- Urine analysis

- Urine culture

- CBC, basic metabolic panel

- Renal and bladder ultrasound

Following urethroplasty, patients should be monitored for a minimum of 1 year, since the vast majority of recurrences occur within 1 year.

Because of the high rate of recurrence following dilation and other endoscopic approaches, the provider must maintain a high index of suspicion for recurrence when the patient presents with obstructive voiding symptoms or urinary tract infection.

One study has proposed that elevated levels of soluble urokinase-type plasminogen activator receptor (SuPAR) in seminal plasma might be useful as a marker for MAGI.

MAGI can be diagnosed when there are two or more factors present that meet criteria defined by the World Health Organization (WHO):

At the present time, there is one temporary prostatic stent that has received U.S. Food and Drug Administration (FDA) approval. The Spanner

temporary prostatic stent maintains urine flow and allows natural voluntary urination. The prostatic stent is a completely internal device and can be inserted and removed as easily as a Foley catheter. It permits normal bladder and sphincter functioning and can be worn comfortably by patients. The temporary prostatic stent is typically used to help patients maintain urine flow after procedures that cause prostatic swelling, such as brachytherapy, cryotherapy, TUMT, TURP. It has also become an effective differential diagnostic tool for identifying poor bladder function separate from prostatic obstruction.

In females, meatal stenosis can usually be treated in the physician's office using local anesthesia to numb the area and dilating (widening) the urethral opening with special instruments.

In boys, it is treated by a second surgical procedure called meatotomy in which the meatus is crushed with a straight mosquito hemostat and then divided with fine-tipped scissors. Recently, home-dilatation has been shown to be a successful treatment for most boys.

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.

Penile color duplex doppler ultrasound can help with preoperative planning to minimize bulbar necrosis.

When an infant is born with PSH, the most difficult management decision has often been the sex assignment, since genitalia with this degree of ambiguity do not resemble either sex very well with respect to looks or function. Many infants with PPHS have been assigned and raised as female despite presence of testes and XY chromosomes.

Nearly all parents of infants with PPSH are offered surgical reconstruction, to either further masculinize or feminize the external genitalia.

Treatment with testosterone postnatally does not close the urethra or change the malformation, but in some cases may enlarge the penis slightly.

A physical exam of the genitals is applied to ensure that there are no anatomical problems. The urine will be examined for the presence of semen. If there are no sperm in the urine, it may be due to damage to the prostate as a result of surgery or prior radiation therapy.

Diagnosis is usually by way of a urinalysis performed on a urine specimen that is obtained shortly after ejaculation. In cases of retrograde ejaculation, the specimen will contain an abnormal level of sperm.

Especially in case of "orgasmic anejaculation", anejaculation can often be confused with retrograde ejaculation, and they share some fundamental aspects of the cause. Urinalysis is used to distinguish between them.

It is considered a form of 5-alpha-reductase deficiency involving SRD5A2.

The main treatment for isolated epispadias is a comprehensive surgical repair of the genito-urinary area usually during the first 7 years of life, including reconstruction of the urethra, closure of the penile shaft and mobilisation of the corpora. The most popular and successful technique is known as the modified Cantwell-Ransley approach. In recent decades however increasing success has been achieved with the complete penile disassembly technique despite its association with greater and more serious risk of damage.

Surgery is usually recommended for hypospadias, with the goal to restore normal appearance and function to the penis. A urinary opening that is not surrounded by glans tissue is more likely to “spray” the urine, which can cause a man to sit to urinate because he cannot reliably stand and hit the toilet. Downward curvature of the penis can impair sexual activity as an adult.

Surgery extends the urinary channel to the end of the penis, straightens bending, and corrects the foreskin abnormality by either circumcision or by repairing it to look normal (“prepucioplasty”), depending on the desire of care-givers.

When the hypospadias is third degree (penoscrotal), or has associated birth defects such as chordee or cryptorchidism, the best management can be a more complicated decision. A karyotype and endocrine evaluation should be performed to detect intersex conditions or hormone deficiencies. If the penis is small, testosterone or human chorionic gonadotropin (hCG) injections may be given to enlarge it before surgery.

Surgical repair of severe hypospadias may require multiple procedures and mucosal grafting. Preputial skin is often used for grafting and circumcision should be avoided before repair. In a minority of patients with severe hypospadias, surgery produces unsatisfactory results, such as scarring, curvature, or formation of urethral fistulas, diverticula, or strictures. A fistula is an unwanted opening through the skin along the course of the urethra, and can result in urinary leakage or an abnormal stream. A diverticulum is an "outpocketing" of the lining of the urethra which interferes with urinary flow and may result in posturination leakage. A stricture is a narrowing of the urethra severe enough to obstruct flow. Reduced complication rates even for third-degree repair (e.g., fistula rates below 5%) have been reported in recent years from centers with the most experience, and surgical repair is now performed for the vast majority of infants with hypospadias.

Hypospadias repair is done under general anesthesia, most often supplemented by a nerve block to the penis or a caudal block to reduce the general anesthesia needed, and to minimize discomfort after surgery.

Many techniques have been used during the past 100 years to extend the urinary channel to the correct location. Today, the most common operation, known as the tubularized incised plate or “TIP” repair, rolls the urethral plate from the low meatus to the end of the glans. This procedure can be used for all distal hypospadias repairs, with complications afterwards expected in less than 10% of cases.

Less consensus exists regarding proximal hypospadias repair. TIP repair can be used when the penis is straight or has mild downward curvature, with success in 85%. Alternatively, the urinary channel can be reconstructed using the foreskin, with reported success in from 55% to 75%.

Most distal and many proximal hypospadias are corrected in a single operation. However, those with the most severe condition having a urinary opening in the scrotum and downward bending of the penis are often corrected in a two-stage operation. During the first operation the curvature is straightened. At the second, the urinary channel is completed.

Vaginal prolapses are treated according to the severity of symptoms. They can be treated:

- With conservative measures (changes in diet and fitness, Kegel exercises, pelvic floor physical therapy.

- With a pessary, a rubber or silicon device fitted to the patient which is inserted into the vagina and may be retained for up to several months. Pessaries are a good choice of treatment for women who wish to maintain fertility, are poor surgical candidates, or who may not be able to attend physical therapy. Pessaries require a provider to fit the device, but most can be removed, cleaned, and replaced by the woman herself. Pessaries should be offered to women considering surgery as a non-surgical alternative.

- With surgery (for example native tissue repair, biological graft repair, absorbable and non-absorbable mesh repair, colpopexy, colpocleisis). Surgery is used to treat symptoms such as bowel or urinary problems, pain, or a prolapse sensation. According to the Cochrane Collaboration review (2016) current evidence does not support the use of transvaginal surgical mesh repair compared with native tissue repair for anterior compartment prolapse owing to increased morbidity. Safety and efficacy of many newer meshes is unknown. The use of a transvaginal mesh in treating vaginal prolapses is associated with side effects including pain, infection, and organ perforation. According to the FDA, serious complications are "not rare." A number of class action lawsuits have been filed and settled against several manufacturers of TVM devices.

Congenital anomalies like cryptorchidism, renal agenesis/dysplasia, musculoskeletal and cardiopulmonary anomalies are also common (>50% cases), hence evaluation of the patient for internal anomalies is mandatory.

Although aphallia can occur in any body type, it is considered a substantially more troublesome problem with those who have testes present, and has in the past sometimes been considered justification for assigning and rearing a genetically male infant as a girl. After the theory in the 1950s that gender as a social construct was purely nurture and so an individual child could be raised early on and into one gender or the other regardless of their genetics or brain chemistry. Intersex people generally advocate harshly against coercive genital reassignment however, and encourage infants to be raised choosing their own gender identity. The nurture theory has been largely abandoned and cases of trying to rear children this way have not proven to be successful transitions.

In newborn period or infancy, feminizing operations are recommended for treatment of penile agenesis, but after 2 years, as sexual identification of the patients has appeared, it is advised to perform masculinizing operations in order not to disturb the child psychologically.

Recent advances in surgical phalloplasty techniques have provided additional options for those still interested in pursuing surgery.

Even with successful surgery, patients may have long-term problems with:

- incontinence, where serious usually treated with some form of continent urinary diversion such as the Mitrofanoff

- depression and psycho-social complications

- sexual dysfunction

Use of male condoms or female condoms may help prevent the spread of trichomoniasis, although careful studies have never been done that focus on how to prevent this infection. Infection with Trichomoniasis through water is unlikely because "Trichomonas vaginalis" dies in water after 45–60 minutes, in thermal water after 30 minutes to 3 hours and in d urine after 5–6 hours.

Currently there are no routine standard screening requirements for the general U.S. population receiving family planning or STI testing. The Centers for Disease Control and Prevention (CDC) recommends Trichomoniasis testing for females with vaginal discharge and can be considered for females at higher risk for infection or of HIV-positive serostatus.

The advent of new, highly specific and sensitive trichomoniasis tests present opportunities for new screening protocols for both men and women. Careful planning, discussion, and research are required to determine the cost-efficiency and most beneficial use of these new tests for the diagnosis and treatment of trichomoniasis in the U.S., which can lead to better prevention efforts.

A number of strategies have been found to improve follow-up for STI testing including email and text messaging as reminders of appointments.

Patients with erectile dysfunction (ED) and PFUDD or patients with PFUDD and traumatic disruption of the dorsal arteries are susceptible to bulbar urethral necrosis. These patients need tubularized substitution urethroplasty, which is replacement of the bulbar urethra with a various number of tubularized flaps ranging from scrotal skin to sigmoid colon (and others).

It is a rare condition, with only approximately 60 cases reported as of 1989, and 75 cases as of 2005. However, due to the stigma of intersex conditions and the issues of keeping accurate statistics and records among doctors, it is likely there are more cases than reported.

Strictures tend to be diagnosed based on difficulty with insertion and manipulation during sialendoscopy, or by sialography or ultrasound.

A bifid penis (or double penis) is a rare congenital defect where two genital tubercles develop.

Historically, males born with a bifid penis often underwent sex reassignment surgery, due to the difficulty of penile reconstruction. They were raised as girls, and often had reconstructive surgery to make them phenotypically female, coupled with female hormone replacement therapy. However, in recent years, this practice has fallen under heavy scrutiny due to both a high frequency of sexual dysfunction in gender converted children, and more advanced penile reconstruction techniques.

Many male marsupials naturally have a bifid penis, with left and right prongs that they insert into multiple vaginal canals simultaneously.

In one report, about 20% of individuals with mealtime syndrome had strictures upon sialography. For unknown reasons, strictures seem to be more common in females.