The exact cause of VIN is unknown. Studies are being done to determine the cause of VIN. The following factors have been associated with VIN:

- HPV (Human Papilloma Virus)

- HSV-2 (Herpes simplex Virus - Type 2)

- Smoking

- Immunosuppression

- Chronic vulvar irritation

- Conditions such as Lichen Sclerosus

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 term Vulvar intraepithelial neoplasia (VIN) refers to particular changes that can occur in the skin that covers the vulva. VIN is not cancer, and in some women it disappears without treatment. If the changes become more severe, there is a chance that cancer might develop after many years, and so it is referred to as a precancerous condition.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

Bowenoid papulosis is a cutaneous condition characterized by the presence of pigmented verrucous papules on the body of the penis. They are associated with human papillomavirus, the causative agent of genital warts. The lesions have a typical dysplastic histology and are generally considered benign, although a small percentage will develop malignant characteristics.

It is considered as a pre-malignant condition. Other terms used to describe the condition are: Erythroplasia of Queyrat, Squamous cell carcinoma in situ and Bowen’s disease. The term "Bowenoid papulosis" was coined in 1977 by Kopf and Bart and is named after dermatologist John Templeton Bowen.

The term “intraepithelial neoplasia” defines a premalignant intraepithelial change.

On the vulva it is termed VIN (vulvar or vulval intraepithelial neoplasia); on the penis, PIN (penile intraepithelial neoplasia); and on or around the anus, AIN (anal intraepithelial neoplasia). The terminology has been very confusing and it is now recommended that the terms Bowen’s disease, erythroplasia of Queyrat, and bowenoid papulosis should not be used for lesions in the anogenital area. However, dermatologists still recognize a distinct clinical variant, bowenoid papulosis, characterized by discrete papules in a younger age group and a tendency for spontaneous regression. Additionally, some authorities believe that erythroplasia of Queyrat and Bowen’s disease remain useful terms in men.

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.

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.

Hyperplasia may be due to any number of causes, including increased demand (for example, proliferation of basal layer of epidermis to compensate skin loss), chronic inflammatory response, hormonal dysfunctions, or compensation for damage or disease elsewhere. Hyperplasia may be harmless and occur on a particular tissue. An example of a normal hyperplastic response would be the growth and multiplication of milk-secreting glandular cells in the breast as a response to pregnancy, thus preparing for future breast feeding.

Perhaps the most interesting and potent effect IGF has on the human body is its ability to cause hyperplasia, which is an actual splitting of cells. By contrast, hypertrophy is what occurs, for example, to skeletal muscle cells during weight training and steroid use and is simply an increase in the size of the cells. With IGF use, one is able to cause hyperplasia which actually increases the number of muscle cells present in the tissue. Weight training with or without anabolic steroid use enables these new cells to mature in size and strength. It is theorized that hyperplasia may also be induced through specific power output training for athletic performance, thus increasing the number of muscle fibers instead of increasing the size of a single fiber.

Sclerosing lymphangitis is a skin condition characterized by a cordlike structure encircling the coronal sulcus of the penis, or running the length of the shaft, that has been attributed to trauma during vigorous sexual play.

Nonvenereal sclerosing lymphangitis is a rare penile lesion consisting of a minimally tender, indurated cord involving the coronal sulcus and occasionally adjacent distal penile skin. This disorder most often occurs after vigorous sexual activity and resolves spontaneously.

Etiology of Sclerosing lymphangitis is unknown but has been postulated to be secondary to thrombosis of lymphatic vessels. Spontaneous recovery can occur anywhere within a couple weeks to several months.

Although it is commonly recommended the patient abstain from any sexual activitiy during the recovery, there is no evidence that this expedites recovery nor that not abstaining worsens the condition.

Hyperplasia (from ancient Greek ὑπέρ "huper", "over" + πλάσις "plasis", "formation"), or hypergenesis, is an increase in the amount of organic tissue that results from cell proliferation. It may lead to the gross enlargement of an organ and the term is sometimes confused with benign neoplasia or benign tumor.

Hyperplasia is a common preneoplastic response to stimulus. Microscopically, cells resemble normal cells but are increased in numbers. Sometimes cells may also be increased in size (hypertrophy). Hyperplasia is different from hypertrophy in that the adaptive cell change in hypertrophy is an increase in the "size" of cells, whereas hyperplasia involves an increase in the "number" of cells.

Summer penile syndrome is usually caused by chigger bites on the penis. Majority of cases occur in the summer months, with the clothing associated with warmer weather making penis-insect contact more likely.

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.

In an embryo, the conversion of the gonads into testicles in males-to-be and into ovaries in females-to-be is the function of Leydig cells. In testicular agenesis, this process fails. Penile agenesis can be caused by testicular agenesis. Testes are the sole producer of 5-alpha dihydrotestosterone (5aDHT) in the male body. Where the gonads fail to metamorphose into testes, there is no 5aDHT. Therefore, the masculising process that builds the genital tubercle, the precursor to the penis, is stillborn. When this happens, the child is born with both penile and testicular agenesis and is known by the slang term "nullo". This combination of both conditions is estimated to occur in between 20-30 million male births.

Penile agenesis can exist independently after full testicular development; in this case its cause is unknown.

Summer penile syndrome (also known as 'Lions Mane Penis') is a seasonal pediatric medical condition characterized by redness, swelling (Edema), and itching (pruritus) of the penile skin.

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