Most cases involve a small and bifid penis, which requires surgical closure soon after birth, often including a reconstruction of the urethra. Where it is part of a larger exstrophy, not only the urethra but also the bladder (bladder exstrophy) or the entire perineum (cloacal exstrophy) are open and exposed on birth, requiring closure.

Despite the similarity of name, an epispadias is not a type of hypospadias, and involves a problem with a different set of embryologic processes.

Women can also have this type of congenital malformation. Epispadias of the female may occur when the urethra develops too far anteriorly, exiting in the clitoris or even more forward. For females, this may not cause difficulty in urination but may cause problems with sexual satisfaction. Frequently, the clitoris is bifurcated at the site of urethral exit, and therefore clitoral sensation is less intense during sexual intercourse due to frequent stimulation during urination. However, with proper stimulation, using either manual or positional techniques, clitoral orgasm is definitely possible.

PPSH usually consists of:

- a phallus midway in size between penis and clitoris,

- a chordee tethering it to the perineum,

- a urethral opening usually on the perineum (the hypospadias),

- and an incompletely closed urogenital opening, which resembles a small and shallow vagina.

Testes are often palpable in the scrotum or inguinal canals, and the karyotype is XY. In most cases there are no internal female structures such as a uterus or other Müllerian duct derivatives.

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.

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.

At birth, the inner layer of the foreskin is sealed to the glans penis. The foreskin is usually non-retractable in early childhood, and can be as late as 18.

Medical associations advise not to retract the foreskin of an infant, in order to prevent scarring. Some argue that non-retractability may "be considered normal for males up to and including adolescence." Hill states that full retractability of the foreskin may not be achieved until late childhood or early adulthood. A Danish survey found that the mean age of first foreskin retraction is 10.4 years.

Rickwood, as well as other authors, has suggested that true phimosis is over-diagnosed due to failure to distinguish between normal developmental non-retractability and a pathological condition. Some authors use the terms "physiologic" and "pathologic" to distinguish between these types of phimosis; others use the term "non-retractile foreskin" to distinguish this developmental condition from pathologic phimosis.

In some cases a cause may not be clear, or it may be difficult to distinguish physiological phimosis from pathological if an infant appears to be in pain with urination or has obvious ballooning of the foreskin with urination or apparent discomfort. However, ballooning does not indicate urinary obstruction.

In women a comparable condition is known as "clitoral phimosis" whereby the clitoral hood cannot be retracted, limiting exposure of the glans clitoridis.

Aphallia is a congenital malformation in which the phallus (penis or clitoris) is absent. It is the female counterpart of penile agenesis and testicular agenesis. The word is derived from the Greek "a-" for "not", and "phallos" for "penis". It is classified as an intersex condition.

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

Phimosis is a condition in which the foreskin of the penis cannot be pulled back past the glans. A balloon-like swelling under the foreskin may occur with urination. In teenagers and adults, it may result in pain during an erection, but is otherwise not painful. Those affected are at greater risk of inflammation of the glans, known as balanitis, and other complications.

In young children, it is normal to not be able to pull back the foreskin. In more than 90% of cases, this inability resolves by the age of seven, and in 99% of cases by age 16. Occasionally, phimosis may be caused by an underlying condition such as scarring due to balanitis or balanitis xerotica obliterans. This can typically be diagnosed by seeing scarring of the opening of the foreskin.

Typically, it resolves without treatment by the age of three. Efforts to pull back the foreskin during the early years of a young male’s life should not be attempted. For those in whom the condition does not improve further time can be given or a steroid cream may be used to attempt to loosen the tight skin. If this method, combined with stretching exercises, is not effective, then other treatments such as circumcision may be recommended. A potential complication of phimosis is paraphimosis, where the tight foreskin becomes trapped behind the glans. The word is from the Greek "phimos" (φῑμός), meaning "muzzle".

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.

Aphallia has no known cause. It is not linked to deficient hormone amounts or action, but rather to a failure of the fetal genital tubercle to form between 3 and 6 weeks after conception. The urethra of an affected child opens on the perineum.

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.

A chordee may be caused by an underlying condition, such as a disorder of sex development or an intersex condition, or from a complication of circumcision, though some medical professionals do not consider it to be true chordee because the corporal bodies are normally formed. However, not all congenital chordee includes abnormal corpora, and case reports of damage to the corpus cavernosum from circumcision are noted in the literature; particularly as a complication of local anesthetic.

Micropenis is an unusually small penis. A common criterion is a dorsal (measured on top) erect penile length of at least 2.5 standard deviations smaller than the mean human penis size, or smaller than about for an adult when compared with an average erection of . The condition is usually recognized shortly after birth. The term is most often used medically when the rest of the penis, scrotum, and perineum are without ambiguity, such as hypospadias. Micropenis occurs in about 0.6% of males.

A popping or cracking sound, significant pain, swelling, immediate loss of erection leading to flaccidity, and skin hematoma of various sizes are commonly associated with the sexual event.

Paraphimosis is usually caused by medical professionals or parents who handle the foreskin improperly: The foreskin may be retracted during penile examination, penile cleaning, urethral catheterization, or cystoscopy; if the foreskin is left retracted for a long period, some of the foreskin tissue may become edematous (swollen with fluid), which makes subsequent reduction of the foreskin difficult.

Chordee () is a condition in which the head of the penis curves downward or upward, at the junction of the head and shaft of the penis. The curvature is usually most obvious during erection, but resistance to straightening is often apparent in the flaccid state as well. In many cases but not all, chordee is associated with hypospadias. This is not the same condition as Peyronie's disease, which involves curvature of the shaft of the penis most commonly due to injury during adult life.

Penile fracture is rupture of one or both of the "tunica albuginea", the fibrous coverings that envelop the penis's "corpora cavernosa". It is caused by rapid blunt force to an erect penis, usually during vaginal intercourse, or aggressive masturbation. It sometimes also involves partial or complete rupture of the urethra or injury to the dorsal nerves, veins and arteries.

Symptoms can include:

- First signs – small red erosions on the glans

- Redness of the foreskin

- Redness of the penis

- Other rashes on the head of the penis

- Foul smelling discharge

- Painful foreskin and penis

Of the abnormal conditions associated with micropenis, most are conditions of reduced prenatal androgen production or effect, such as abnormal testicular development (testicular dysgenesis), Klinefelter syndrome, Leydig cell hypoplasia), specific defects of testosterone or dihydrotestosterone synthesis (17,20-lyase deficiency, 5α-reductase deficiency), androgen insensitivity syndromes, inadequate pituitary stimulation (gonadotropin deficiency), and other forms of congenital hypogonadism. Micropenis can also occur as part of many genetic malformation syndromes that do not involve the sex chromosomes. It is sometimes a sign of congenital growth-hormone deficiency or congenital hypopituitarism. Several homeobox genes affect penis and digit size without detectable hormone abnormalities.

In addition, in utero exposure to some estrogen based fertility drugs like diethylstilbestrol (DES) has been linked to genital abnormalities and/or a smaller than normal penis.

After evaluation to detect any of the conditions described above, micropenis can often be treated in infancy with injections of various hormones, such as human chorionic gonadotropin and testosterone.

Most eight- to fourteen-year-old boys referred for micropenis do not have the micropenis condition. Such concerns are usually explained by one of the following:

- a penis concealed in suprapubic fat (extra fat around the mons pubis)

- a large body and frame for which a prepubertal penis simply appears too small

- delayed puberty with every reason to expect good future growth

Paraphimosis is an uncommon medical condition in which the foreskin of a penis becomes trapped behind the glans penis, and cannot be "reduced" (pulled back to its normal flaccid position covering the glans). If this condition persists for several hours or there is any sign of a lack of blood flow, paraphimosis should be treated as a medical emergency, as it can result in gangrene.

Males with penile agenesis but normal testes are of otherwise normal male appearance.

Males with testicular agenesis tend not to produce the reproductive hormone 5aDHT at any stage of their lives. As a result, they tend toward prepubescent appearance, with infantile skin texture, developing little body hair particularly in the crotch area, even vellus hair. Without genitalia of either sex, the perineum is therefore left smooth. Also muscular development is retarded and testicular agenetics are of rather frail build with short limbs and small hands and feet.

However certain male features are results of other male gender-marker hormones, "androgens", which develop male secondary sex characteristics, among which features are the deepening of the voice and facial hair.

Erythroplasia of Queyrat is a squamous-cell carcinoma of the glans penis (head of the penis) or inner prepuce (foreskin) in males, and the vulvae in females. It mainly occurs in uncircumcised males, over the age of 40. Erythroplasia of Queyrat may also occur on the anal mucosa or the oral mucosa.

Some sources state that this condition is synonymous with Bowen's disease, however generally speaking Bowen's disease refers to carcinoma in situ of any location on the skin such as the lower leg. Like Bowen's disease, erythroplasia of Queyrat is associated with human papillomavirus 16 and is a precursor for invasive squamous-cell carcinoma.

It is named for French dermatologist Louis Queyrat (1856-1933), who was head of the dermatology service of l'Hôpital Ricord, a venereal hospital in Paris, now Hôpital Cochin.

Amputation of the penis can be either partial or complete. Often self-inflicted by people with psychiatric disorders, it may be occur with other trauma, such as in an assault or a mechanical accident. These injuries are treated by re-implantation if possible, with or without anastomosis of the vasculature to restore erectile function; skin necrosis and loss of sensation are common complications after treatment. Microsurgery on the vasculature decreases the risk of necrosis significantly. Klingsor syndrome is a psychiatric disorder that causes self-harm, which can involve the penis. Paranoid schizophrenia, eating disorders, and psychotic breaks can also be associated with penile injury. In some cases, transgender people who are not able to access genital surgery may self-amputate their penis. Favorable prognostic factors for replantation of amputated penises include short ischemic time and a clean incision (as opposed to a crush injury or ragged incision).

Replantation of an amputated penis can be done up to 24 hours after the injury, though fewer than 16 hours of cold ischemia or 6 hours of warm ischemia leads to the best outcomes. If replantation is not possible or desired, a penile stump can be closed and phalloplasty could be performed later.

Degloving and avulsion injuries involve the removal of the penis skin, which is a serious medical emergency. Treatment of these injuries involves either closure of the torn skin, or a skin graft to replace the skin lost in the injury. Skin grafts are constructed to attempt to preserve erectile function and sensation.