Defining Intersex

Yellow flag with a purple circle. The intersex flag.
   The two intersex flags

“Intersex” is a general term used to describe people who are born with reproductive or sexual anatomy that does not fit the typical definitions of female or male. For example, a person might appear to be female on the outside at birth, but have mostly male-typical reproductive organs inside. In another case, a person may be born with genitalia that seems to fall in-between the usual male and female types—for example, a female may be born with a noticeably large clitoris or lack a vaginal opening, or a male may be born with a notably small penis, or with a scrotum that is divided so that it has formed more like labia. A person may be born with mosaic genetics, so that some of their cells have XX chromosomes and some of them have XY.1 Some characteristics that are often associated with the development of intersex individuals include hormonal variations during pregnancy, genetic mutations, and environmental toxins.

Purple, white, blue, and pink striped flag. The intersex flag.
   The two intersex flags

Though we speak of intersex as an inborn condition, intersex anatomy isn’t always apparent at birth. Sometimes a person is not found to have intersex anatomy until they reach the age of puberty, experience infertility issues as an adult, or passes away and is autopsied. Some people live and die with intersex anatomy without anyone (including themselves) ever knowing.

In Western society, most intersex infants undergo hormonal and surgical treatment so that they can appear as either male or female. As you will read later, these treatments are often given without the consent of the intersex child, and are often psychologically harmful. Despite these treatments and the fact that these intersex characteristics are not always physically identifiable, intersex individuals are very often confronted with gender identity issues, ridiculed by peers, and experience fertility problems. Intersex individuals are not abnormal in any way and should not be stigmatized on the basis of their genitalia. Intersex individuals should be treated with the same respect as everyone else.

Hermaphroditism is not to be confused with intersexuality! The term “hermaphrodite” implies that a person has both full male and full female external and internal genitalia; whereas intersex simply means that a person doesn’t have typically female or male genitalia. There is an intersex condition called “true hermaphroditism,” but this refers to the internal reproductive structures: the ovaries and the testes are present. However, these are not fully functional and are often not fully developed.

Furthermore, transgender and transsexual are also different from intersex. People who identify as transgender or transsexual are usually people who are born with typical male or female anatomy but feel as though they have been born into the “wrong body.” For example, a person who identifies as transgender may have typical female anatomy but feel like a male and want to live as a male. Some may seek to become male by taking hormones or electing to undergo sex reassignment surgery. People who have intersex conditions have anatomy that is not considered typically male or female, and most seek medical attention because they or their parents notice something unusual about their bodies. In contrast, people who are transgender have an internal experience of gender identity that is different from their assigned sex.

A person holding a baby. They are facing each other and touching nose-to-nose.

Which variations of sexual anatomy count as intersex?

The intersex symbol.

In practice, different people have different answers to this question. This is not surprising because intersex isn’t a discrete or natural category; intersex is a socially constructed category that reflects normal biological variation. In most human cultures, sex categories are simplified into male and female in order to simplify social interactions and maintain order. Therefore, nature does not decide where the category of “male” of “female” ends and the category of “intersex” begins. There is a lot of variation in how genitalia develop person-to-person. Nature provides us with a wide spectrum of forms, onto which our society imposes two absolute categories of male and female. It is typically left to medical practitioners to decide how small a penis has to be, or how unusual a combination of parts has to be before it counts as intersex.

About 1 in 1,500 to 2,000 births result in a child born so noticeably atypical in terms of genitalia that a specialist in sex differentiation is called in.1 There are theories that the number is in fact higher than that because many people are born with subtler forms of sex anatomy variations, some of which won’t show up until later in life, especially when the variation is internal.

Typical Development of Fetal Genitalia

An anatomical diagram of the development of fetal genitals.

In the womb, all fetuses’ genitals start off the same way: they are the same until the baby is nine weeks old, then they start to differentiate. This means that the structures of male and female genitalia stem from the same basic structures, and therefore share many similarities. At nine weeks, the fetus’s genitals are made up of a genital bud (also called genital tubercle), at the top, a urogenital fold, found directly underneath the bud, a labioscrotal development (also called genital swelling) which surrounds the urogenital fold, and a urogenital sinus, which is surrounded by the urogenital fold.

– In typical female babies, the genital bud becomes the shaft and glans of the clitoris, the urogenital fold becomes the labia minora and the vaginal opening, the labioscrotal development becomes the labia majora and mons pubis, and the urogenital sinus becomes the urethral and vaginal orifices.2

– In typical male babies, the genital bud becomes the glans of the penis, the urogenital fold becomes the shaft of the penis and the penile urethra, the labioscrotal development becomes the scrotum, and the urogenital sinus becomes the prostate and structures that make up the shaft of the penis.2

Common Intersex Genitalia

This is not intended to be an exhaustive list of intersex conditions! There are many variations of intersexuality and genitalia. These are, however, the most common presentations of ambiguous genitalia.


Clitoromegaly is a condition in which the clitoris is larger than what is typically considered “normal.” It may have the size of a penis.3 The distinction between what is considered a “normal” sized clitoris and an abnormally large one is somewhat arbitrary. Typically, if the clitoris is double the average size, the patient is considered to have clitoromegaly. Congenital adrenal hyperplasia (CAH), polycystic ovarian syndrome (PCOS), or endocrine (hormonal) disorders are the usual causes. No serious health issues are related to having an enlarged clitoris.


Hypospadias is a condition in which the opening of the urethra is found on the underside of the penis instead of at the tip. The abnormal opening can form anywhere from just below the end of the penis to the scrotum. There are different degrees of hypospadias; some can be minor and some more severe:

Three different penises with hypospadia. One subcoronal, one midshaft, and one penoscrotal penis.
  • Subcoronal – The opening of the urethra is located near the head of the penis.
  • Midshaft – The opening of the urethra is located along the shaft of the penis.
  • Penoscrotal – The opening of the urethra is located where the penis and scrotum meet.4

Most cases of hypospadias require surgery to correct the defect, as it can cause difficult urination, severe curvature of the penis, or difficulties during sexual intercourse.

Vaginal Agenesis or Müllerian Agenesis

Vaginal agenesis, also referred to as Müllerian aplasia, is the congenital absence of the vagina, uterus, or both. A vagina can usually be created nonsurgically with successive vaginal dilations. In some cases, the complete absence of the vagina does require surgery. A uterine remnant may be present, which can cause abdominal pain during menstruation, as the blood cannot exit the body properly through the vaginal canal. However, this uterus is usually not properly formed or functional and is often completely absent. Because of this, carrying children is often not an option. The ovaries, given their separate embryological source, are normal in structure and function.5


Aphallia is a congenital malformation in which the phallus (penis or clitoris) is completely absent. This is a very rare condition, with only 75 cases reported as of 2005.6 This happens when no genital bud or tubercle forms during early pregnancy. A urethra may need to be constructed. Surgery is usually required for this condition.


  1. “What is intersex?” Intersex Society of North America. Web.
  2. “Urogenital Development” Duke Medicine. Web. October 22, 2013.
  3. “What is clitoromegaly?” WiseGEEK. Web.
  4. “Facts about Hypospadias” Centers for Disease Control and Prevention, CDC. Web. October 16, 2014.
  5. “Müllerian Agenesis: Diagnosis, Management, and Treatment” The American Congress of Obstetricians and Gynecologists, ACOG. Web. May 2013.
  6. “Male gender assignment in aphallia: a case report and review of the literature” Web.

Last Updated: 11 November 2015.