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.

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.

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.

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.

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

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.

Examples of functional problems of the reproductive system include:

- Impotence - The inability of a male to produce or maintain an erection.

- Hypogonadism - A lack of function of the gonads, in regards to either hormones or gamete production.

- Ectopic pregnancy - When a fertilized ovum is implanted in any tissue other than the uterine wall.

- Hypoactive sexual desire disorder - A low level of sexual desire and interest.

- Female sexual arousal disorder - A condition of decreased, insufficient, or absent lubrication in females during sexual activity

- Premature ejaculation - A lack of voluntary control over ejaculation.

- Dysmenorrhea - Is a medical condition of pain during menstruation that interferes with daily activities

Penile agenesis is a birth defect in humans, occurring about once in 5–6 million male births, in which a male child is born without a penis.

A partner condition is testicular or gonadal agenesis. This is when a male child is born without gonads and consequently develops no testes. Penile agenesis occurs often as a consequence of Testicular agenesis, but the reverse is never the case. Most patients in both cases have no known family history and usually have an otherwise normal male anatomy.

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

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.

A reproductive system disease is any disease of the reproductive system.

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.

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.

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.

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.

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.

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.

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

Erectile dysfunction (ED), also known as impotence, is a type of sexual dysfunction characterized by the inability to develop or maintain an erection of the penis during sexual activity. Erectile dysfunction can have psychological consequences as it can be tied to relationship difficulties and self-image.

The most important organic causes of impotence are cardiovascular disease and diabetes, neurological problems (for example, trauma from prostatectomy surgery), hormonal insufficiencies (hypogonadism) and drug side effects. Psychological impotence is where erection or penetration fails due to thoughts or feelings (psychological reasons) rather than physical impossibility; this is somewhat less frequent but can often be helped. In psychological impotence, there is a strong response to placebo treatment.

Besides treating the underlying causes such as potassium deficiency or arsenic contamination of drinking water, the first line treatment of erectile dysfunction consists of a trial of PDE5 inhibitor (such as sildenafil). In some cases, treatment can involve prostaglandin tablets in the urethra, injections into the penis, a penile prosthesis, a penis pump or vascular reconstructive surgery.

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".

Surgical intervention for a number of conditions may remove anatomical structures necessary to erection, damage nerves, or impair blood supply. Erectile dysfunction is a common complication of treatments for prostate cancer, including prostatectomy and destruction of the prostate by external beam radiation, although the prostate gland itself is not necessary to achieve an erection. As far as inguinal hernia surgery is concerned, in most cases, and in the absence of postoperative complications, the operative repair can lead to a recovery of the sexual life of patients with preoperative sexual dysfunction, while, in most cases, it does not affect patients with a preoperative normal sexual life.

ED can also be associated with bicycling due to both neurological and vascular problems due to compression. The increase risk appears to be about 1.7-fold.

Concerns that use of pornography can cause erectile dysfunction have not been substantiated in epidemiological studies according to a recent literature review. However, another review and case studies article maintains that use of pornography does indeed cause erectile dysfunction, and critiques the previously described literature review.

Recurrent bouts of balanitis may cause scarring of the preputial orifice; the reduced elasticity may lead to pathologic phimosis.