Adapted from the chapter, Sex and Intersex.

"Intersex" describes many different ways in which sex development goes wrong. Where sex manifests in genes, hormones, primary sex characteristics, and secondary sex characters, variation in sex occurs in all these areas too.

Because sex and gender are different, an intersex person is not necessarily transgender. Intersex advocates are quick to point out that intersex does not fit under the transgender umbrella as gender identities like transexual and genderqueer. I agree wholeheartedly because intersex refers to sex and not gender and because "transgender" is a voluntary group and we don't force people to join. Intersex people were formerly referred to as "hermaphrodites" but is now depreciated for being derogatory and clinically problematic.

To get an idea of the diversity, here are some of the more common intersex conditions. For more detail, I recommend the Intersex Society of North America and their website www.isna.org.

Klinefelters Syndrome (XXY)

The most common intersex case is Klinefelter's syndrome where the karyotype is XXY affecting one in every 500 people. A cell will only permit one X chromosome to be active and the other X is de-activated. and is part of normal  functioning in XX cells. In Klinefelter cases, the same process happens which minimizes effects. In the same category is the karyotype XXXY where two Xs are de-activated. Thus, Klinefelter patients look almost exactly like people with an XY karyotype: male. The only significant effect is being sterile but the additional X creates some relatively minor effects. They usually identify as male and some identify as transgender.

Turner Syndrome (XO)

Turner syndrome is similar to to Klinefelter's but features a karyotype with one too few chromosomes instead of one too many. Affected people have only one X chromosome and no Y chromosome (written as "XO"). They are phenotypical females. One in 50 every conceptions have Turner syndrome but only 2% survive pregnancy.(www.isna.org/faq/conditions/turner)  Again, because of regular X inactivation, the person is able to live without great effects after birth.

Mosaicism

Typically, every cell in a single body (except the gametes) have identical genes. Mosaicism is a case where this does not happen. Mosaicism is not always intersex, only when the cells have differing karyotypes. A person may be literally any combination of XX, XY, XO, XXY, etc. Likewise, its affects come in every possibility. Mosaicism is notoriously difficult to measure because, if present, performing a karyotype test will yield different results depending on which part of the body is tested. For example, someone with XX/XY mosaicism with 99% XX cells would need (statistically) 100 tests before finding an XY cell. It is therefore impossible to measure incidence. Josef Kirchner is a ex-trans poster child turned genderqueer who is XY/XO.

One type of mosaicism is mixed gonadal dysgenesis where the gonads are radically different. One may be an ovary and the other a teste or one may be an ovo-teste, a gonad with some ovarian cells and some testicular cells.

Congenital Adrenal Hyperplasia (CAH)

Commonly called CAH, congenital adrenal hyperplasia occurs in XX karyotypes where an abnormally high amount of masculine hormones are present. The levels of hormones differ from person to person but their genitals and gonads react to the hormones the same way as males. The genital tubercle is larger than typical clitorises and may be as a large as a penis and/or the labia may resemble a scrotum and sometimes even seal the vagina. This is called "ambiguous genitalia." They may also have increased body hair, malformed ovum leading to infertility. and may be mistaken for boys. In all cases there are serious health risks. 10% of intersex people with CAH identify as transgender.PEDIATRICS Vol. 118 No. 2 August 2006, pp. 753-757 as seen on http://pediatrics.aappublications.org/cgi/content/full/118/2/753 

Androgen Insensitivity Syndrome (AIS)

AIS occurs in XY karyotypes with a genetic condition which disables the body from reacting to androgens. They have partially formed and undescended testes and a small vagina but are otherwise phenotypically female. Lacking ovaries, they are infertile and do not menstruate. AIS occurs in 1 in 10,000 XY karyotypes. Their gender identity is always female.By "always" I mean I have l never heard of a male or trans identified AIS patient and intersex organizations like ISNA say the same. 

A variant of AIS is partial AIS (PAIS) where the body only partly reacts to androgens. This can cause ambiguous genitalia or non-intersex male infertility. People with PAIS may identify as male or female. There are other intersex conditions with the same effects of AIS but different cause where the SRY gene is absent of mutated and unable to function.

5-ARD

5-alpha-reductase deficiency is a problem in XY karyotypes where the androgen DHT is not  created. The genitals of such a person can be typically male, typically female, or anywhere in between. Benig a genetically inherited trait, the incidence varies. In the Dominican Republic it exists in 1 in 90 males. Most people identify as female with a few identifying as male and a few as bigender or genderqueer.

Genital malformation

Various simpler intersex condition exist where everything is normal except that the genitals display a single abnormality. These include a very small penis (micropenis), a very large clitoris (clitoromegaly), the absence of either a clitoris or penis (aphallia) or hypospadias. Hypospadias affects males in whom the urethra has not moved to the tip of the penis and is somewhere in between the tip of the penis and its original location between the labia (which have formed into the scrotum).

Chart

Note: I simplified some data. Regarding genitals, "Any" includes penis and scrotum, clitoris and vagina, or ambiguous. Regarding gonads, "Any" includes ovaries, testes, or ovo-testes. Regarding second sex characteristics, "Any" includes traditional female, traditional male, or anywhere in between. Regardnig gender identity, "Any" includes women, men, genderqueer or bigender. Of course, any intersex person may have a genderqueer or bigender identity. The only identities listed are the most common. Prevalence based on a global population of 6.5 billion people.