Variations in genitalia

When a child’s genitals are not easily discernible as either female or male, they are said to have variations in genitalia. Most children born with anatomical variations are otherwise healthy, but it can be a scary time for parents.

Variations in genitalia occur in about one in every 4,500 newborns, making it hardly rare. There isn’t just one cause. It can sometimes be quite difficult to determine the sex of the child, but tests are performed to check chromosomes and check for internal reproductive structures.

Variations in genitalia are now being referred to more and more as one such Difference of Sexual Development (DSD), which refers to situations whereby a child’s genetics, hormones, internal organs, or external genitalia are atypical.

The old terminology for variations in genitalia is ‘ambiguous genitalia’, however, this name is being phased out as understanding of the many expressions of gender and variations in genitalia expands.

Typical development of foetal genitalia

When a foetus is developing, the tissue that becomes the gonads – the ovaries or testes – is not differentiated, meaning, it’s all the same, and has the potential to be either ovaries or testes.

Biological sex is determined by our father’s sperm (sperm is either male or female). Gender is usually chosen or assumed at birth based on genital presentation.

We have 46 chromosomes in every cell in our body, 23 pairs. The 23rd pair is used for sex (and often gender) determination, with females having two X chromosomes (XX) and males having one X and one Y chromosome (XY).

The presence of the SRY gene causes an undifferentiated gonad (tissue that could go either way) to become testes at around the six-week mark of foetal development.

Regression of the female reproductive tract then occurs in a typical biological male, causing the formation of the penis, scrotum, and urethra, and later, the descent of the testes into the scrotum.

In a typical biological female, the absence of the SRY gene causes the gonad to turn into an ovary, and the female reproductive tract continues to develop the uterus and fallopian tubes. The male organs regress.

How do variations in genitalia occur?

It is during this foetal development process that an unknown genetic blip occurs that influences the development of variations of genitals. Other congenital differences may exist within the same child, though usually the child is otherwise healthy.

What causes variations in genitalia?

The cause may not be able to be determined without further testing, since there is a wide variety of conditions that can cause varied, atypical genitalia. Sometimes no cause can be found and it is deemed a biological ‘accident’.

Children are classified as follows:

Sex chromosome DSD means children who have a mixture of 45 X, 46 XX, 46 XY, and 46 XXY. Some of these kids will have both ovarian and testicular tissue, and both male and female internal organs.


46 XY DSD occurs when the chromosomes are 46 XY, but the testes are undeveloped (gonadal dysgenesis), certain hormones are not produced, or the body either doesn’t respond, or only partially responds, to hormones.

There are three conditions to represent these three states: complete androgen insensitivity syndrome, partial androgen insensitivity, and 5-alpha reductase deficiency.

  1. Complete androgen insensitivity syndrome (CAIS) – children who have 46 XY karyotype and typical female external genitalia (does not affect female genitalia, but affects male genitalia)
  2. Partial androgen insensitivity (PAIS) – children who have 46 XY karyotype, with female or male external genitalia, or features of both external genitalia. This condition is also called androgen insensitivity syndrome, since the body does not respond to androgens (testosterone). Mothers with this gene have a 50 per cent chance of passing it on to their female children.
  3. 5-alpha reductase deficiency (5ARD) – children who have 46 XY karyotype, genital ambiguity, with enzyme 5-alpha reductase being deficient. This enzyme converts testosterone into dihydrotestosterone (DHT), which is necessary to fully complete the masculinisation of a male foetus. Carrier parents have a 12.5 per cent chance of passing it on, since each parent carries a copy of the gene and transmits it to the child.


The 46 XX DSD combination occurs when the foetus is exposed to excess male hormones after a malfunction of their own adrenal glands – this is because they have the SRY gene, and have developed testes, but this can also occur due to external exposure to male hormones in utero.

46 XX DSD has been discussed regarding the driver of sexual orientation/preferences and gender identity. The most common cause of 46 XX DSD is congenital adrenal hyperplasia (CAH).

Congenital adrenal hyperplasia (CAH)

Congenital adrenal hyperplasia is one of the more common causes of variations in genitals and must be quickly diagnosed and treated as soon as possible to avoid a very sick baby. It happens in about one in every 15,000 live births.

CAH is caused by a defect in enzyme 21-hydroxylase, a steroid hormone synthesis pathway in the adrenal gland. There is an issue creating steroid hormones in the adrenal gland, and this interferes with proper adrenal gland function and testosterone production.

Carrier parents have a 25 per cent chance of passing it on to a child. CAH can result in females becoming masculinised and having varied genitalia, but not males. If the enzyme deficiency is found before or during pregnancy, medication can be given to lessen the effects of the enzyme deficiency if the foetus is female, though this is still experimental.

A second type of CAH is called salt-losing and can be lethal due to blood levels of sodium and potassium changing in the newborn.

Treatment is available and lethal outcomes can be avoided if detected early enough. Males and females are equally affected. Other rare enzyme problems that can result in CAH exist.

Determining gender in children with varied genitalia

First, an examination will be conducted to search for clues. The medical history will include the mother’s pregnancy and any family history of other atypical anatomical variations.

Diagnostic procedures can include hormone tests, ultrasounds, and screening for CAH. Assigning a gender can be complicated without obvious genital signs. More often now, children with varied genital appearance can make their own choice when they are able.

There is much more room than ever before for our kids to be themselves, and not have to have their gender decided for them.

These children need caregivers and healthcare practitioners who support them psychologically, which may include special support services throughout life and care taken with use of language.


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Jessica Lloyd - Vulvovaginal Specialist Naturopathic Practitioner, BHSc(N)

Jessica is a degree-qualified naturopath (BHSc) specialising in vulvovaginal health and disease, based in Melbourne, Australia.

Jessica is the owner and lead naturopath of My Vagina, and is a member of the:

  • International Society for the Study of Vulvovaginal Disease (ISSVD)
  • International Society for the Study of Women's Sexual Health (ISSWSH)
  • National Vulvodynia Association (NVA) Australia
  • New Zealand Vulvovaginal Society (ANZVS)
  • Australian Traditional Medicine Society (ATMS)