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.

The appearance of XX males can fall into one of three categories: 1) males that have normal internal and external genitalia, 2) males with external ambiguities, and 3) males that have both internal and external genital ambiguities (true hermaphrodites). External genital ambiguities can include hypospadias, micropenis, and clitoromegaly. On average, the appearance of XX males differs from that of an XY male in that they are smaller in height and weight. Most XX males have small testes, are sterile, and have an increase in maldescended testicles compared to XY males. Some XX male individuals have decreased amounts of body hair and decreased libido. Individuals with this condition sometimes have feminine characteristics, with varying degrees of gynecomastia but with no intra-abdominal Müllerian tissue. According to research at the University of Oklahoma health science centers, despite XX males exhibiting feminine characteristics, their behaviours are usually representative of masculinity in their culture.

Anorchia (or anorchism) is an XY disorder of sex development in which individuals have both testes absent at birth. Within a few weeks of fertilization, the embryo develops rudimentary gonads (testes), which produce hormones responsible for the development of the reproductive system. If the testes fail to develop within eight weeks, the baby will develop female genitalia (see Swyer syndrome). If the testes begin to develop but are lost or cease to function between eight and 10 weeks, the baby will have ambiguous genitalia when it is born. However, if the testes are lost after 14 weeks, the baby will have partial male genitalia with the notable absence of gonads.

Tests include observable lack of testes, low testosterone levels (typical female levels), elevated follicle stimulating hormone and luteinizing hormone levels, XY karyotype, ultrasound or magnetic resonance imaging showing absent gonadal tissue, low bone density, low anti-Müllerian hormone levels, and surgical exploration for evidence of male gonadal tissue.

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.

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".

Treatment includes androgen (testosterone) supplementation to artificially initiate puberty, testicular prosthetic implantation, and psychological support. Gender Dysphoria may result in anorchic individuals who are assigned male at birth and raised as male despite lacking the necessary masculinizing hormones during prenatal, childhood, and adolescent development. Anorchic individuals who have a female identity may be administered estrogen alone in place of testosterone as no androgen blockers are necessary due to the lack of gonads.

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.

XX male syndrome is a rare congenital condition where an individual with a female genotype has phenotypically male characteristics that can vary between cases. In 90% of these individuals the syndrome is caused by unequal crossing over between X and Y chromosomes during meiosis in the father, and results in the X chromosome containing the SRY gene, as opposed to the Y chromosome where it is normally found. When the X with the SRY gene combines with a normal X from the mother during fertilization, the result is an XX male. Less common are SRY-negative XX males which can be caused by a mutation in an autosomal or X chromosomal gene. The masculinization of XX males is variable.

This syndrome is diagnosed through various detection methods and occurs in approximately 1:20 000 newborn males, making it less common than Klinefelter syndrome. Treatment is medically unnecessary, although some individuals choose to undergo treatments to make them appear more male or female. It is also called de la Chapelle syndrome, for Albert de la Chapelle, who characterized it in 1972.

Mutations that result in some residual 21-hydroxylase activity cause milder disease, traditionally termed simple virilizing CAH (SVCAH). In these children the mineralocorticoid deficiency is less significant and salt-wasting does not occur. However, genital ambiguities are possible.

Gonadal dysgenesis is any congenital developmental disorder of the reproductive system characterized by a progressive loss of germ cells on the developing gonads of an embryo. This loss leads to extremely hypoplastic (underdeveloped) and dysfunctioning gonads mainly composed of fibrous tissue, hence the name streak gonads—i.e., a form of aplasia in which the ovary is replaced by functionless tissue. The accompanying hormonal failure also prevents the development of secondary sex characteristics in either sex, resulting in a sexually infantile female appearance and infertility.

The first type of gonadal dysgenesis discovered was Turner syndrome.

The condition may be due to:

- Turner syndrome, and its variations (i.e. mosaicism)

- XX gonadal dysgenesis, also pure gonadal dysgenesis, 46,XX

- Swyer syndrome, also pure gonadal dysgenesis, 46,XY

- Perrault syndrome, XX gonadal dysgenesis + sensorineural hearing loss

- Mixed gonadal dysgenesis

- Exposure to environmental endocrine disruptors

45,X/46,XY mosaicism, also known as X0/XY mosaicism and mixed gonadal dysgenesis, is a rare disorder of sex development in humans associated with sex chromosome aneuploidy and mosaicism of the Y chromosome. This is called a mosaic karyotype because, like tiles in mosaic floors or walls, there is more than one type of cell.

The clinical manifestations are highly variable, ranging from partial virilisation and ambiguous genitalia at birth, to patients with a completely male or female gonads. Most individuals with this karyotype have apparently normal male genitalia, and a minority with female genitalia, with a significant number of individuals showing genital abnormalities or intersex characteristics. A significantly higher than normal number of other developmental abnormalities are also found in individuals with X0/XY mosaicism. Psychomotor development is normal.

Congenital adrenal hyperplasia due to 21-hydroxylase deficiency (21-OH CAH), in all its forms, accounts for over 95% of diagnosed cases of congenital adrenal hyperplasia, and "CAH" in most contexts refers to 21-hydroxylase deficiency. An overview of the other types of CAH is presented in the main article.

Although similar in some ways to true hermaphroditism, the conditions can be distinguished histologically and by karyotyping. The observable characteristics (phenotype) of this condition are highly variable, ranging from gonadal dysgenesis in males, to Turner-like females and phenotypically normal males. The phenotypical expression may be ambiguous, intersex, or male or female depending on the extent of the mosaicism. The most common presentation of 45,X/46,XY karyotype is phenotypically normal male, next being genital ambiguity.

There is a range of chromosomal anomalies within 45,X/46,XY where the variations are very complex, and the actual result in living individuals is often not a simple picture. Most patients with this karyotype are known to have abnormal gonadal histology and heights considerably below their genetic potential. High gonadotropin levels have been described in both male and female patients, as well as low levels of testosterone in male patients. Dosage loss of SHOX gene is commonly associated with short stature. Psychomotor development is normal.

As the gonads may not be symmetrical, the development of the Müllerian duct and Wolffian duct may be asymmetrical, too. Because of the presence of dysgenetic gonadal tissue and Y chromosome material, there is a high risk of the development of a gonadoblastoma.

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.

Many men who were born with undescended testes have reduced fertility, even after orchiopexy in infancy. The reduction with unilateral cryptorchidism is subtle, with a reported infertility rate of about 10%, compared with about 6% reported by the same study for the general population of adult men.

The fertility reduction after orchiopexy for bilateral cryptorchidism is more marked, about 38%, or 6 times that of the general population. The basis for the universal recommendation for early surgery is research showing degeneration of spermatogenic tissue and reduced spermatogonia counts after the second year of life in undescended testes. The degree to which this is prevented or improved by early orchiopexy is still uncertain.

There is a small body of research on the psychology of cryptorchidism, that attempts to determine whether this condition can cause lasting psychological problems. The psychological research on cryptorchism consists of only a few case reports and small studies. This research also has serious methodological problems: major variables are completely uncontrolled, such as the small physical stature of many cryptorchid boys, and the psychological effects of corrective surgery.

Existing research indicates that boys with undescended testicles do not tend to be gender-disordered, effeminate, or pre-homosexual. A disturbed self-image forms only when the family dynamics are destructive to developing male self-esteem. Such pathogenic attitudes were found in parents who focused on the boy’s genital defect as a sign of his presumed effeminacy. However, when the cryptorchism is surgically corrected a healthy masculinity becomes possible. The basic sexual normality of these boys was confirmed in a small retrospective study that tested adolescent boys several years after their condition was surgically repaired. They had developed into fairly well-adjusted teenagers without special sexual or gender problems, and with no distinctive traits of psychopathological relevance.

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

Congenital adrenal hyperplasia (CAH) are any of several autosomal recessive diseases resulting from mutations of genes for enzymes mediating the biochemical steps of production of mineralocorticoids, glucocorticoids or sex steroids from cholesterol by the adrenal glands (steroidogenesis).

Most of these conditions involve excessive or deficient production of sex steroids and can alter development of primary or secondary sex characteristics in some affected infants, children, or adults.

The symptoms of CAH vary depending upon the form of CAH and the sex of the patient. Symptoms can include:

Due to inadequate mineralocorticoids:

- vomiting due to salt-wasting leading to dehydration and death

Due to excess androgens:

- functional and average sized penis in cases involving extreme virilization (but no sperm)

- ambiguous genitalia, in some females, such that it can be initially difficult to identify external genitalia as "male" or "female".

- early pubic hair and rapid growth in childhood

- precocious puberty or failure of puberty to occur (sexual infantilism: absent or delayed puberty)

- excessive facial hair, virilization, and/or menstrual irregularity in adolescence

- infertility due to anovulation

- clitoromegaly, enlarged clitoris and shallow vagina

Due to insufficient androgens and estrogens:

- Undervirilization in XY males, which can result in apparently female external genitalia

- In females, hypogonadism can cause sexual infantilism or abnormal pubertal development, infertility, and other reproductive system abnormalities

Congenital adrenal hyperplasia due to 3β-hydroxysteroid dehydrogenase deficiency is an uncommon form of congenital adrenal hyperplasia (CAH) resulting from a mutation in the gene for one of the key enzymes in cortisol synthesis by the adrenal gland, 3β-hydroxysteroid dehydrogenase (3β-HSD) type II (HSD3B2). As a result, higher levels of 17OH-pregnenolone appear in the blood with adrenocorticotropic hormone (ACTH) challenge, which stimulates adrenal corticosteroid synthesis.

There is a wide spectrum of clinical presentations of 3β-HSD CAH, from mild to severe forms. The uncommon severe form results from a complete loss of enzymatic activity and manifests itself in infancy as salt wasting due to the loss of mineralocorticoids. Milder forms resulting from incomplete loss of 3β-HSD type II function do not present with adrenal crisis, but can still produce virilization of genetically female infants and undervirilization of genetically male infants. As a result, this form of primary hypoadrenalism is the only form of CAH that can cause ambiguous genitalia in both genetic sexes.

The mineralocorticoid aspect of severe 3β-HSD CAH is similar to those of 21-hydroxylase deficiency. Like other enzymes involved in early stages of both aldosterone and cortisol synthesis, the severe form of 3β-HSD deficiency can result in life-threatening salt-wasting in early infancy. Salt-wasting is managed acutely with saline and high-dose hydrocortisone, and long-term fludrocortisone.

Vaginal atresia can sometimes be diagnosed by physical examination soon after birth. A child with vaginal atresia often has other congenital abnormalities and other tests such as x-ray and tests to evaluate the kidney are done. Findings in adolescents may include abdominal pain, difficulty voiding, and backache, but most present with amenorrhea. Difficulties with sexual intercourse can suggest atresia. In the event that the condition is not caught shortly after birth, vaginal atresia becomes more evident when no menstrual cycle is occurs. If vaginal atresia is suspected by the doctor, a blood test may also be request for any of the previously mentioned syndromes, a magnetic resonance imaging (MRI) test, or an ultrasound. A regular evaluation of children born with an imperforate anus or anorectal malformation should be paired with the assessment of the results from these tests.

Symptoms and signs in the newborn can be sepsis, abdominal mass, and respiratory distress. Other abdominopelvic or perineal congenital anomalies frequently prompt radiographic evaluation in the newborn, resulting in a diagnosis of coincident vaginal atresia. Symptoms for vaginal atresia include cyclical abdominal pain, the inability to start having menstrual cycles, a small pouch or dimple where a vaginal opening should be, and pelvic mass when the upper vagina becomes filled with menstrual blood. Signs and symptoms of vaginal atresia or vaginal agenesis can often go unnoticed in females until they reach the age of menstruation. Women may also experience some form of abdominal pain or cramping.

Lipoid congenital adrenal hyperplasia is an endocrine disorder that is an uncommon and potentially lethal form of congenital adrenal hyperplasia (CAH). It arises from defects in the earliest stages of steroid hormone synthesis: the transport of cholesterol into the mitochondria and the conversion of cholesterol to pregnenolone—the first step in the synthesis of all steroid hormones. Lipoid CAH causes mineralocorticoid deficiency in affected infants and children. Male infants are severely undervirilized causing their external genitalia to look feminine. The adrenals are large and filled with lipid globules derived from cholesterol.