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.

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.

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.

Hypospadias is among the most common birth defects in the world and is said to be the second-most common birth defect in the male reproductive system, occurring once in every 250 males.

Due to variations in the reporting requirements of different national databases, data from such registries cannot be used to accurately determine either incidence of hypospadias or geographical variations in its occurrences.

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.

A problem for people with penile agenesis is the absence of a urinary outlet. Before genital metamorphosis, the urethra runs down the anal wall, to be pulled away by the genital tubercle during male development. Without male development this does not occur. The urethra can be surgically redirected to the rim of the anus immediately after birth to enable urination and avoid consequent internal irritation from urea concentrate. In such cases, the perineum may be left devoid of any genitalia, male or female.

A working penis transplant on to an agenetic patient has never been successful. Only one major penis graft was successfully completed. This occurred in China and the patient shortly rejected it on psychological grounds. However a full female or agenetic to male transplant is not yet facilitated to fulfil full reproductive functions.

On March 18, 2013, it was announced that Andrew Wardle, a British man born without a penis, was going to receive a pioneering surgery to create a penis for him. The surgeons hope to "fold a large flap of skin from his arm — complete with its blood vessels and nerves — into a tube to graft onto his pubic area." If the surgery goes well, the odds of starting a family are very good.

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

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.

The principal treatment of chordee is surgery in infancy, usually by a pediatric urologist. With chordees caused by circumcision, the preferred method of surgical treatment is a z-plasty. The preferred time for surgery is between the ages of 6 and 18 months and correction is usually successful.

Growth of the penis both before birth and during childhood and puberty is strongly influenced by testosterone and, to a lesser degree, the growth hormone. However, later endogenous hormones mainly have value in the treatment of micropenis caused by hormone deficiencies, such as hypopituitarism or hypogonadism.

Regardless of the cause of micropenis, if it is recognized in infancy, a brief course of testosterone is often prescribed (usually no more than 3 months). This usually induces a small amount of growth, confirming the likelihood of further growth at puberty, but rarely achieves normal size. No additional testosterone is given during childhood, to avoid unwanted virilization and bone maturation. (There is also some evidence that premature administration of testosterone can lead to reduced penis size in the adult.)

Testosterone treatment is resumed in adolescence only for boys with hypogonadism. Penile growth is completed at the end of puberty, similar to the completion of height growth, and provision of extra testosterone to post-pubertal adults produces little or no further growth.

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

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.

Because hormone treatment rarely achieves average size, several surgical techniques similar to phalloplasty for penis enlargement have been devised and performed; but they are not generally considered successful enough to be widely adopted and are rarely performed in childhood.

In extreme cases of micropenis, there is barely any shaft, and the glans appears to sit almost on the pubic skin. From the 1960s until the late 1970s, it was common for sex reassignment and surgery to be recommended. This was especially likely if evidence suggested that response to additional testosterone and pubertal testosterone would be poor. With parental acceptance, the boy would be reassigned and renamed as a girl, and surgery performed to remove the testes and construct an artificial vagina. This was based on the now-questioned idea that gender identity was shaped entirely from socialization, and that a man with a small penis can find no acceptable place in society.

Johns Hopkins Hospital, the center most known for this approach, performed twelve such reassignments from 1960 to 1980, most notably that of David Reimer (whose penis was destroyed by a circumcision accident), overseen by John Money. By the mid-1990s, reassignment was less often offered, and all three premises had been challenged. Former subjects of such surgery, vocal about their dissatisfaction with the adult outcome, played a large part in discouraging this practice. Sexual reassignment is rarely performed today for severe micropenis (although the question of raising the boy as a girl is sometimes still discussed.) (See "History of intersex surgery" for a fuller discussion.)

A treatment option for micropenis is the insertion of a subcutaneous soft silicone implant under the penile skin. The procedure was developed by urologist James J. Elist.

Webbed penis, also called penis palmatus or penoscrotal fusion, is an acquired or congenital condition in which the scrotal skin extends onto the ventral penile shaft. The penile shaft is buried in scrotum or tethered to the scrotal midline by a fold or web of skin. The urethra and erectile bodies are usually normal. Webbed penis is usually asymptomatic, but the cosmetic appearance is often unacceptable. This condition may be corrected by surgical techniques.

In the congenital form, the deformity represents an abnormality of the attachment between the penis and the scrotum; the penis, the urethra, and the remainder of the scrotum typically are normal.

Webbed penis may also be acquired (iatrogenic) after circumcision or other penile surgery, resulting from excessive removal of ventral penile skin; the penis can retract into the scrotum, resulting in secondary phimosis (trapped penis).

One procedure for webbed penis is the insertion of a subcutaneous soft silicone implant under the penile skin. The procedure was developed by urologist James J. Elist.

It is usually considered a congenital malformation of unknown cause. Since at an early stage of fetal development the penis is curved downward, it has been proposed that chordee results from an arrest of penile development at that stage.

The curvature of a chordee can involve

1. tethering of the skin with urethra and corpora of normal size;

2. curvature induced by fibrosis and contracture of the fascial tissue (Buck's fascia or dartos) surrounding the urethra;

3. disproportionately large corpora in relation to the urethral length without other demonstrable abnormality of either; or

4. a short, fibrotic urethra that tethers the penis downward (the least common type).

Severe degrees of chordee are usually associated with hypospadias, but mild degrees of curvature may occur in many otherwise normal males. When the curved penis is small and accompanied by hypospadias, deficiency of prenatal androgen effect can be inferred.

People with either penile agenesis or testicular agenesis, but not both, usually continue as males throughout their lives. Historically, people with both penile and testicular agenesis were raised as females and eventually underwent sex reassignment surgery, despite having a normal 46,XY male karyotype and no female sexual characteristics. This practice was controversial, and many individuals decided to live as males again when they reached puberty or their early twenties. The New Zealand sexologist John Money was the principle theorist who argued that boys born without an "adequate" penis, or who lost their penis in an accident, should be raised as sex reassigned girls. The book "As Nature Made Him" chronicles the disastrous results of the application of Money's theories in the Bruce/Brenda case. The anatomy underlying the failure of these cases is not well understood. In most males, the development of the embryo into a female is prevented by Anti-Müllerian hormones. These hormones are commonly believed to be created in the testes, but they nevertheless still appear to be produced in male embryos lacking testes.

Ultrasound examination is able to depict the tunica albuginea tear in the majority of cases (as a hypoechoic discontinuity in the normally echogenic tunica). In a study on 25 patients, Zare Mehrjardi et al. concluded that ultrasound is unable to find the tear just when it is located at the penile base. In their study magnetic resonance imaging (MRI) accurately diagnosed all of the tears (as a discontinuity in the normally low signal tunica on both T1- and T2-weighted sequences). They concluded that ultrasound should be considered as the initial imaging method, and MRI can be helpful in cases that ultrasound does not depict any tear but clinical suspicious for fracture is still high. In the same study, authors investigated accuracy of ultrasound and MRI for determining the tear location (mapping of fracture) in order to performing a tailored surgical repair. MRI was more accurate than ultrasound for this purpose, but ultrasound mapping was well correlated with surgical results in cases the tear was clearly visualized on ultrasound exam.

Penile fracture is a medical emergency, and emergency surgical repair is the usual treatment. Delay in seeking treatment increases the complication rate. Non-surgical approaches result in 10–50% complication rates including erectile dysfunction, permanent penile curvature, damage to the urethra and pain during sexual intercourse, while operatively treated patients experience an 11% complication rate.

In some cases, retrograde urethrogram may be performed to rule out concurrent urethral injury.

Procedure for buried penis is the insertion of a subcutaneous soft silicone implant under the penile skin. The procedure was developed by urologist James J. Elist.

It is analyzed in several ways:

- Obtaining full erections at some times, such as nocturnal penile tumescence when asleep (when the mind and psychological issues, if any, are less present), tends to suggest that the physical structures are functionally working.

- Other factors leading to erectile dysfunction are diabetes mellitus (causing neuropathy).

There are no formal tests to diagnose erectile dysfunction. Some blood tests are generally done to exclude underlying disease, such as hypogonadism and prolactinoma. Impotence is also related to generally poor physical health, poor dietary habits, obesity, and most specifically cardiovascular disease such as coronary artery disease and peripheral vascular disease. Therefore, a thorough physical examination is helpful, in particular the simple search for a previously undetected groin hernia since it can affect sexual functions in men and is easily curable.

A useful and simple way to distinguish between physiological and psychological impotence is to determine whether the patient "ever" has an erection. If "never", the problem is likely to be physiological; if "sometimes" (however rarely), it could be physiological or psychological. The current diagnostic and statistical manual of mental diseases (DSM-IV) has included a listing for impotence.

- Duplex ultrasound:Duplex ultrasound is used to evaluate blood flow, venous leak, signs of atherosclerosis, and scarring or calcification of erectile tissue. Injecting prostaglandin, a hormone-like stimulator produced in the body, induces the erection. Ultrasound is then used to see vascular dilation and measure penile blood pressure.

- Penile nerves function:Tests such as the bulbocavernosus reflex test are used to determine if there is sufficient nerve sensation in the penis. The physician squeezes the glans (head) of the penis, which immediately causes the anus to contract if nerve function is normal. A physician measures the latency between squeeze and contraction by observing the anal sphincter or by feeling it with a gloved finger inserted past the anus.

- Nocturnal penile tumescence (NPT):It is normal for a man to have five to six erections during sleep, especially during rapid eye movement (REM). Their absence may indicate a problem with nerve function or blood supply in the penis. There are two methods for measuring changes in penile rigidity and circumference during nocturnal erection: snap gauge and strain gauge. A significant proportion of men who have no sexual dysfunction nonetheless do not have regular nocturnal erections.

- Penile biothesiometry:This test uses electromagnetic vibration to evaluate sensitivity and nerve function in the glans and shaft of the penis.

- Dynamic infusion cavernosometry (DICC): technique in which fluid is pumped into the penis at a known rate and pressure. It gives a measurement of the vascular pressure in the corpus cavernosum during an erection.

- Corpus cavernosometry:Cavernosography measurement of the vascular pressure in the corpus cavernosum. Saline is infused under pressure into the corpus cavernosum with a butterfly needle, and the flow rate needed to maintain an erection indicates the degree of venous leakage. The leaking veins responsible may be visualized by infusing a mixture of saline and x-ray contrast medium and performing a cavernosogram. In Digital Subtraction Angiography (DSA), the images are acquired digitally.

- Magnetic resonance angiography (MRA): This is similar to magnetic resonance imaging. Magnetic resonance angiography uses magnetic fields and radio waves to provide detailed images of the blood vessels. Doctors may inject a "contrast agent" into the patient's bloodstream that causes vascular tissues to stand out against other tissues. The contrast agent provides for enhanced information regarding blood supply and vascular anomalies.

Physiologic phimosis, common in males 10 years of age and younger, is normal, and does not require intervention. Non-retractile foreskin usually becomes retractable during the course of puberty.

If phimosis in older children or adults is not causing acute and severe problems, nonsurgical measures may be effective. Choice of treatment is often determined by whether circumcision is viewed as an option of last resort to be avoided or as the preferred course.

Paraphimosis can be avoided by bringing the foreskin back into its normal, forward, non-retracted position after retraction is no longer necessary (for instance, after cleaning the glans penis or placing a Foley catheter). Phimosis (both pathologic and normal childhood physiologic forms) is a risk factor for paraphimosis; "physiologic" phimosis resolves naturally as a child matures, but it may be advisable to treat "pathologic" phimosis via long-term stretching or elective surgical techniques (such as preputioplasty to loosen the preputial orifice or circumcision to amputate the foreskin tissue partially or completely).

The foreskin responds to the application of tension to cause expansion by creating new skin cells though the process of mitosis. The tissue expansion is permanent. Non-surgical stretching of the foreskin may be used to widen a narrow, non-retractable foreskin. Stretching may be combined with the use of a steroid cream. Beaugé recommends manual stretching for young males in preference to circumcision as a treatment for non-retractile foreskin because of the preservation of sexual sensation.

Paraphimosis can often be effectively treated by manual manipulation of the swollen foreskin tissue. This involves compressing the glans and moving the foreskin back to its normal position, perhaps with the aid of a lubricant, cold compression, and local anesthesia as necessary. If this fails, the tight edematous band of tissue can be relieved surgically with a dorsal slit or circumcision. An alternative method, the Dundee technique, entails placing multiple punctures in the swollen foreskin with a fine needle, and then expressing the edema fluid by manual pressure. According to Ghory and Sharma, treatment by circumcision may be elected as "a last resort, to be performed by a urologist". Other experts recommend delaying elective circumcision until after paraphimosis has been resolved.

Buried penis (also known as hidden penis) is a congenital or acquired condition, in which the penis is partially or completely hidden below the surface of the skin. It can lead to obstruction of urinary stream, poor hygiene, soft tissue infection, phimosis, and inhibition of normal sexual function. Congenital causes include maldevelopment of penile shaft skin, whereas acquired conditions include morbid obesity, overlaying abdominal fat, or penile injury. Adults with a buried penis will either live with their condition or undergo weight-loss programs. However, weight-loss programs are slow and often do not "unbury" the penis; furthermore, poor hygiene from pooling of urine can lead to soft tissue infection. Patients will eventually need definitive reconstructive surgery and more urgent surgery if infection is present. Surgeons who manage this condition are either reconstructive urologic surgeons or plastic surgeons.

5α-Reductase is an enzyme that converts testosterone to 5α-dihydrotestosterone (DHT) in peripheral tissues. These enzymes also participate in the creation of such neurosteroids as allopregnanolone and THDOC, convert progesterone into dihydroprogesterone (DHP), and convert deoxycorticosterone (DOC) into dihydrodeoxycorticosterone (DHDOC). 5-ARD is biochemically characterized by low to low-normal levels of testosterone and decreased levels of DHT, creating a higher testosterone/DHT ratio.

DHT is a potent androgen, and is necessary for the development of male external genitalia in utero.

The most acute complication is paraphimosis. In this condition, the glans is swollen and painful, and the foreskin is immobilized by the swelling in a partially retracted position. The proximal penis is flaccid. Some studies found phimosis to be a risk factor for urinary retention and carcinoma of the penis.