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.

Penile fractures are the result of rupture of the tunica albuginea. They are fairly rare and can co-occur with partial or complete urethral rupture, though this is rare. Urethral damage occurs in 10–38% of cases. Fractures are treated with emergency surgery, and can be diagnosed with ultrasound, especially in pediatric cases. Penile fractures are caused by trauma to the erect penis, typically by suddenly bending it laterally during penetrative intercourse with the receptive partner on top of the penetrating partner, or during masturbation. They can be diagnosed by the "eggplant sign" and are characterized by a loud popping sound at the time of the injury, the result of the tunica albuginea rupturing. Other symptoms include severe pain, loss of erection, and swelling. Symptoms of urethral injury include hematuria, blood at the meatus, and dysuria. If left untreated, complications result in 28–53% of cases; these include permanent curvature of the penis, fistula, urethral diverticulum, priapism, and erectile dysfunction.

Labial fusion is never present at birth, but rather acquired later in infancy, since it is caused by insufficient estrogen exposure and newborns have been exposed to maternal estrogen "in utero". It typically presents in infants at least 3 months old. Most presentations are asymptomatic and are discovered by a parent or during routine medical examination. In other cases, patients may present with associated symptoms of dysuria, urinary frequency, refusal to urinate, or post-void dribbling. Some patients present with vaginal discharge due to pooling of urine in the vulval vestibule or vagina.

Rupture of the urethra is an uncommon result of penile injury, incorrect catheter insertion, straddle injury, or pelvic girdle fracture. The urethra, the muscular tube that allows for urination, may be damaged by trauma. When urethral rupture occurs, urine may extravasate (escape) into the surrounding tissues. The membranous urethra is most likely to be injured in pelvic fractures, allowing urine and blood to enter the deep perineal space and subperitoneal spaces via the genital hiatus. The spongy urethra is most likely to be injured with a catheter or in a straddle injury, allowing urine and blood to escape into the scrotum, the penis, and the superficial peritoneal space. Urethral rupture may be diagnosed with a cystourethrogram. Due to the tight adherence of the fascia lata, urine from a urethral rupture cannot spread into the thighs.

Labial fusion is a medical condition of the female genital anatomy where the labia minora become fused together. It is generally a pediatric condition.

The condition is known by a number of names, including labial fusion, labial adhesion, labial synechiae, labial agglutination, labial adherence, gynatresia, vulvar fusion, and vulvar synechiae.

Vaginal hypoplasia is the underdevelopment or incomplete development of the vagina. Vaginal hypoplasia can vary in severity from being smaller than normal to being completely absent. The absence of a vagina is a result of vaginal agenesis. Diagnostically, it may look similar to a vaginal obstruction. It is frequently associated with Mayer-Rokitansky-Küstner-Hauser (MRKH) syndrome, in which the most common result is an absent uterus in conjunction with a deformed or missing vagina, despite the presence of normal ovaries and normal external genitalia. It is also associated with cervical agenesis, in which the uterus is present but the uterine cervix is absent.

The presence of unusual lumps in the wall or base of the vagina is always abnormal. The most common of these is Bartholin's cyst. The cyst, which can feel like a pea, is formed by a blockage in glands which normally supply the opening of the vagina. This condition is easily treated with minor surgery or silver nitrate. Other less common causes of small lumps or vesicles are herpes simplex. They are usually multiple and very painful with a clear fluid leaving a crust. They may be associated with generalized swelling and are very tender. Lumps associated with cancer of the vaginal wall are very rare and the average age of onset is seventy years. The most common form is squamous cell carcinoma, then cancer of the glands or adenocarcinoma and finally, and even more rarely, melanoma.

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.

MAGI includes infections (bacterial, viral, fungal etc) involving one or more of the following male genital organs or tracts:

- seminal vesicles (seminal vesiculitis)

- prostate gland (prostatitis)

- vas deferens

- epididymis (epididymitis)

- testicles (orchitis)

- urethra (urethritis)

- Cowper's glands

Male Accessory Gland Infection (MAGI), also known as Male Accessory Gland Inflammation, is a condition with signs of inflammation involving one or more sites in the male genital tract. Diagnosis is made according to parameters defined by the World Health Organisation, and it is particularly made in relation to infectious or inflammatory causes of male infertility.

Although it is usually caused by infection spreading from the urethra, non-infectious causes also exist.

Uterine prolapse is a form of female genital prolapse. It is also called pelvic organ prolapse or prolapse of the uterus (womb).

Risk factors for uterine prolapse include pregnancy, childbirth, chronic increases in intra-abdominal pressure such as lifting, coughing or straining, connective tissue conditions, and damage to or weakness of the muscles.

Treatment may be conservative or surgical and should be based upon patient symptoms and preference.

Post-vasectomy pain syndrome is a chronic and sometimes debilitating genital pain condition that may develop immediately or several years after vasectomy. Because this condition is a syndrome, there is no single treatment method, therefore efforts focus on mitigating/relieving the individual patient's specific pain. When pain in the epididymides is the primary symptom, post-vasectomy pain syndrome is often described as congestive epididymitis.

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.

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.

Vulvovaginal health is the health and sanitation of the human vulva and vagina.

Problems affecting this area include vulva diseases, vaginal diseases and urinary tract infections.

Any of the aforementioned pain conditions/syndromes can persist for years after vasectomy and affect as many as one in three vasectomized men. The range of PVPS pain can be mild/annoying to the less-likely extreme debilitating pain experienced by a smaller number of sufferers in this group. There is a continuum of pain severity between these two extremes. Pain is thought to be caused by any of the following, either singularly or in combination: testicular backpressure, overfull epididymides, chronic inflammation, fibrosis, sperm granulomas, and nerve entrapment. Pain can be present continuously in the form of orchialgia and/or congestive epididymitis or it can be situational, such as pain during intercourse, ejaculation or physical exertion.

A female genital disease is a condition that affects the female reproductive system.

A woman may have vaginal itching or burning and may notice a discharge.

The discharge may be excessive in amounts or abnormal in color(such as yellow, gray, or green).

The following symptoms may indicate the presence of infection:

- Irritation or itching of the genital area

- inflammation (irritation, redness, and swelling caused by the presence of extra immune cells) of the labia majora, labia minora, or perineal area

- vaginal discharge

- foul vaginal odor

- pain/irritation with sexual intercourse

Anal dysplasia is a pre-cancerous condition which occurs when the lining of the anal canal undergoes abnormal changes. It can be classified as low-grade squamous intraepithelial lesions (LSIL) and high-grade squamous intraepithelial lesions (HSIL).

Most cases are not associated with symptoms, but people may notice lumps in and around the anus.

The uterus (womb) is normally held in place by a hammock of muscles and ligaments. Prolapse happens when the ligaments supporting the uterus become so weak that the uterus cannot stay in place and slips down from its normal position. These ligaments are the round ligament, uterosacral ligaments, broad ligament and the ovarian ligament. The uterosacral ligaments are by far the most important ligaments in preventing uterine prolapse.

The most common cause of uterine prolapse is trauma during childbirth, in particular multiple or difficult births. About 50% of women who have had children develop some form of pelvic organ prolapse in their lifetime. It is more common as women get older, particularly in those who have gone through menopause. This condition is surgically correctable.

The different grade of genital ambiguity is commonly measured by the Prader classification, which ranges, in ascending order of masculinisation, from 1: "female external genitalia with clitoromegaly" through 5: "pseudo-phallus looking like normal male external genitalia".

Alternatively, female genital diseases can be more strictly classified by location of the disease, which, in turn, can be broadly divided between diseases that affect the female internal genitalia and those that affect the female external genitalia.

Anal dysplasia is most commonly linked to human papillomavirus (HPV), a usually sexually-transmitted infection. HPV is the most common sexually transmitted infection in the United States while genital herpes (HSV) was the most common sexually transmitted infection globally.

Clitoromegaly (or macroclitoris) is an abnormal enlargement of the clitoris that is mostly congenital or acquired, though deliberately induced clitoris enlargement as a form of female genital body modification is achieved through various uses of anabolic steroids, including testosterone, and may also be referred to as "clitoromegaly." Clitoromegaly is not the same as normal enlargement of the clitoris seen during sexual arousal.