The use of bioengineered urethral tissue is promising, but still in the early stages. The Wake Forest Institute of Regenerative Medicine has pioneered the first bioengineered human urethra, and in 2006 implanted urethral tissue grown on bioabsorbable scaffolding (approximating the size and shape of the affected areas) in five young (human) males who suffered from congenital defects, physical trauma, or an unspecified disorder necessitating urethral reconstruction. As of March, 2011, all five recipients report the transplants have functioned well.

A permanent urethral stent was approved for use in men with bulbar urethral strictures in 1996, but was recently removed from the market.

A temporary thermoexpandable urethral stent (Memotherm) is available in Europe, but is not currently approved for use in the United States.

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.

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.

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.

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

Accorrding to Frisch & Simonsen (2016), "the foreskin is protective against urinary stricture disease" (meatal stenosis). Frisch & Simonsen (2016) call for a "thorough reassessment of the burden of urethral troubles and other adverse outcomes after non-therapeutic circumcision of boys."

Saeedi "et al". (2017) propose long-term follow-up of circumcision with ultrasonography "to detect meatal stenosis before permanent renal damage occurs."

The protection provided by the foreskin for the glans penis and meatus has been recognized since 1915. In the absence of the foreskin the meatus is exposed to mechanical and chemical irritation from ammoniacal diaper (nappie) that produces blister formation and ulceration of the urethral opening, which eventually gives rise to meatal stenosis (a narrowing of the opening). Meatal stenosis may also be caused by ischemia resulting from damage to the frenular artery during circumcision.

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.

The main infectious agents are Enterobacteriaceae (such as Escherichia coli and Klebsiella), Neisseria gonorrhoeae and Chlamydia trachomatis.

One study has shown that men with MAGI who have lower serum levels of total testosterone tend to have a more complicated form of MAGI, such as involving more than one site, than those with normal levels.

Male Accessory Gland Infection (MAGI), also known as Male Accessory Gland Inflammation, is a condition with signs of inflammation involving one or more sites in the male genital tract. Diagnosis is made according to parameters defined by the World Health Organisation, and it is particularly made in relation to infectious or inflammatory causes of male infertility.

Although it is usually caused by infection spreading from the urethra, non-infectious causes also exist.

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.

Pseudovaginal perineoscrotal hypospadias (PPSH) refers to a configuration of the external genitalia of an infant. In a sense, this configuration is roughly midway between normal male genitalia and normal female genitalia in structure and appearance. It is a relatively common form of genital ambiguity caused by undervirilization of genetic males due to several different intersex conditions.

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.

Hormones potentially increase the size of the penis, and have been used in children with proximal hypospadias who have a smaller penis. Numerous articles report testosterone injections or topical creams increase the length and circumference of the penis. However, few studies discuss the impact of this treatment on the success of corrective surgery, with conflicting results. Therefore, the role, if any, for preoperative hormone stimulation is not clear at this time.

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.

Hypospadias repair can be done in full-term, healthy infants at any time from 3 months of age. Premature babies generally have surgery done at 6 months or older. Using these guidelines, most babies can undergo repair as same-day surgery, without need to stay in the hospital afterwards.

The results of surgery are probably not influenced by the age at which repair is done, but older children are more likely to recall the event. Teens and adults typically spend one night in the hospital after surgery.

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.

Treatment is conservative, mechanical or surgical. Conservative options include behavioral modification and muscle strengthening exercises such as Kegel exercise. Pessaries are a mechanical treatment as they elevate and support the uterus. Surgical options are many and may include a hysterectomy or a uterus-sparing technique such as laparoscopic hysteropexy, sacrohysteropexy or the Manchester operation.

In the case of hysterectomy, the procedure can be accompanied by sacrocolpopexy. This is a mesh-augmented procedure in which the apex of the vagina is attached to the sacrum by a piece of medical mesh material.

A Cochrane Collaboration (2016) review found that sacral colpopexy was associated with lower risk of complications than vaginal interventions, but it was unclear what route of sacral colpopexy should be preferred. No clear conclusion could be reached regarding uterine preserving surgery versus vaginal hysterectomy for uterine prolapse. The evidence does not support use of transvaginal mesh compared to native tissue repair for apical vaginal prolapse. The use of a transvaginal mesh 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.

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

Anal stricture or anal stenosis is a narrowing of the anal canal. It can be caused by a number of surgical procedures including: hemorrhoid removal and following anorectal wart treatment.

Bulbar urethral necrosis is a problem that can occur after a pelvic fracture associated urethral distraction defect (PFUDD).

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.

The treatment depends on the cause. Medications may work for retrograde ejaculation but only in a few cases. Surgery rarely is the first option for retrograde ejaculation and the results have proven to be inconsistent. Medications do not help retrograde ejaculation if there has been permanent damage to the prostate or the testes from radiation. Medications also do not help if prostate surgery has resulted in damage to the muscles or nerves. Medications only work if there has been mild nerve damage caused by diabetes, multiple sclerosis or mild spinal cord injury.

These medications tighten the bladder neck muscles and prevent semen from going backwards into the bladder. However, the medications do have many side effects and they have to be taken at least 1–2 hours prior to sexual intercourse. In many cases, the medications fail to work at the right time because most men are not able to predict when they will have an orgasm.