Extramammary Paget's disease is usually seen in isolation and is associated with an underlying invasive malignancy about 12% of the time. It is associated with an underlying adnexal malignancy about 24% of the time. Paget's disease of the breast is almost always associated with an underlying invasive malignancy, i.e. breast cancer (e.g. mammary ductal carcinoma).

The underlying cause of Peyronie's disease is not well understood, but is thought to be caused by trauma or injury to the penis usually through sexual intercourse or physical activity, although many patients are often unaware of any traumatic event or injury.

A certain degree of curvature of the penis is considered normal, as many men are born with this benign condition, commonly referred to as congenital curvature.

The disease may cause pain; hardened, big, cord-like lesions (scar tissue known as "plaques"); or abnormal curvature of the penis when erect due to chronic inflammation of the tunica albuginea (CITA). Although the popular conception of Peyronie's disease is that it always involves curvature of the penis, the scar tissue sometimes causes divots or indentations rather than curvature. The condition may also make sexual intercourse painful and/or difficult, though it is unclear whether some men report satisfactory or unsatisfactory intercourse in spite of the disorder. It can affect men of any race and age. The disorder is confined to the penis, although a substantial number of men with Peyronie's exhibit concurrent connective tissue disorders in the hand, and to a lesser degree, in the feet. About 30 percent of men with Peyronie's disease develop fibrosis in other elastic tissues of the body, such as on the hand or foot, including Dupuytren's contracture of the hand. An increased incidence in genetically related males suggests a genetic component.

Paget's disease of the vulva, a rare disease, may be a primary lesion or associated with adenocarcinoma originating from local organs such as the Bartholin gland, the urethra, or the rectum and thus be secondary. Patients tend to be postmenopausal.

Paget's disease of the penis may also be primary or secondary, and is even rarer than genital Paget’s disease in women. At least one case has been misdiagnosed as Bowen's disease. Isolated Paget's disease of the penis is extremely rare.

Most patients diagnosed with Paget's disease of the nipple are over age 50, but rare cases have been diagnosed in patients in their 20s. The average age at diagnosis is 62 for women and 69 for men. The disease is rare among both women and men.

It is also known that disruption of the endocrine system by certain chemicals adversely affects the development of the reproductive system and can cause vaginal cancer. Many other reproductive diseases have also been link to exposure to synthetic and environmental chemicals. Common chemicals with known links to reproductive disorders include: lead, dioxins and dioxin-like compounds, styrene, toluene, BPA (Bisphenol A) and pesticides.

The presence of three factors for the prognosis has been suggested, whether there is a palpable mass of the disease, whether lymph nodes are positive and whether there is an underlying malignant cancer.

If there is none of these, the five- and 10-year survival is 85% and 80% respectively, with adjuvant chemotherapy even 95% and 90%. If there is a palpable mass, it is 32% and 31% respectively, with adjuvant chemotherapy (40% and 35%).

Positive lymph-nodes have been positively associated with a palpable mass and affect the prognosis to be now just 28% survival after 10 years (vs 79% without palpable mass and without affected lymph-nodes). Involvement of the lymph nodes does not directly cause any harm, but is merely an indicator of systemic spread.

Furthermore, patients with an identifiable associated underlying breast tumor have a survival rate of 38-40% at five years and a survival rate of 22-33% at 10 years. The death rate of metastatic breast carcinoma in patients with mammary Paget's disease and underlying cancer is 61.3%, with a 10-year cumulative survival rate of 33%.

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.

Examples of congenital abnormalities of the reproductive system include:

- Kallmann syndrome - Genetic disorder causing decreased functioning of the sex hormone-producing glands caused by a deficiency or both testes from the scrotum.

- Androgen insensitivity syndrome - A genetic disorder causing people who are genetically male (i.e. XY chromosome pair) to develop sexually as a female due to an inability to utilize androgen.

- Intersexuality - A person who has genitalia and/or other sexual traits which are not clearly male or female.

Paget's disease may be caused by a slow virus infection (i.e., paramyxoviridae) present for many years before symptoms appear. Associated viral infections include respiratory syncytial virus, canine distemper virus, and the measles virus. However, recent evidence has cast some doubt upon the measles association. Laboratory contamination may have played a role in past studies linking paramyxovirus (e.g. measles) to Paget's disease.

Erythroplakia has an unknown cause but researchers presume it to be similar to the causes of squamous cell carcinoma. Carcinoma is found in almost 40% of erythroplakia. It is mostly found in elderly men around the ages of 65 - 74. It is commonly associated with smoking.

Alcohol and tobacco use have been described as risk factors.

The disease is progressive and slowly worsens with time, although people may remain minimally symptomatic. Treatment is aimed at controlling symptoms, but there is no cure. Any bone or bones can be affected, but Paget's disease occurs most frequently in the spine, skull, pelvis, femur, and lower legs.

Osteogenic sarcoma, a form of bone cancer, is a rare complication of Paget's disease occurring in less than one percent of those affected. The development of osteosarcoma may be suggested by the sudden onset or worsening pain.

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.

Verruciform xanthoma is uncommon, with a female:male ratio of 1:1.1

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.

Median raphe cysts are a cutaneous condition of the penis due to developmental defects near the glans.

Inflammation has many possible causes, including irritation by environmental substances, physical trauma, and infection such as bacterial, viral, or fungal. Some of these infections are sexually transmitted diseases.

It is less common among people who are circumcised as in many cases the foreskin contributes to the disease. Both not enough cleaning and too much cleaning can cause problems. Diabetes can make balanitis more likely, especially if the blood sugar is poorly controlled.

It is important to exclude other causes of similar symptoms such as penile cancer.

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.

A number of medical reports of phimosis incidence have been published over the years. They vary widely because of the difficulties of distinguishing physiological phimosis (developmental nonretractility) from pathological phimosis, definitional differences, ascertainment problems, and the multiple additional influences on post-neonatal circumcision rates in cultures where most newborn males are circumcised. A commonly cited incidence statistic for pathological phimosis is 1% of uncircumcised males. When phimosis is simply equated with nonretractility of the foreskin after age 3 years, considerably higher incidence rates have been reported.

Others have described incidences in adolescents and adults as high as 50%, though it is likely that many cases of physiological phimosis or partial nonretractility were included.

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.

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

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.

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.

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.

Lymphoma is the most common type of blood-related cancer in horses and while it can affect horses of all ages, it typically occurs in horses aged 4–11 years.