this will be important for what I will explain.
http://upload.wikimedia.org/wikipedia/commons/1/13/Steroidogenesis.svgThink of hormone biosynthsis as a river starting with the source Colesterol flowing downstream the river with the primary flow breaking off into ever smaller tributaries as each byproduct is gradually broken down.
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As has been mentioned Poly Cycstic Ovaries can cause unwanted masculinisation however it's not really an intersex disorder.
in the female menstral cycle a folical or lump containing an egg forms on the ovary releasing Progesterone. this lump dissapears normally when the ovum is released but if the ovum cannot be released the folicals will accumilate giving the apperance of cysts that release a hell of alot of progestersone.
Excess progesterone is converted into Testosersone increasing the flow downstream of the biosynthsis pathway Causing masculinisation.
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Another condition that exsists is
Congenital Adrenial Hyperplasia it is an intersex disorder in XX individuals.
Refer to the above chart.
In this disorder the Gene that encodes for the Enzyme. 11-Beta Hydroxylase see it in the minerocordicloids normally produced in the Adrenal glands to the upper right of the image when this happens their cannot be any "flow" from the Progesterone class of hormones into the minerocorciloids. This causes the depletion of those hormones, Cortisol, and Aldosterone. and the resultant precursors are shunted down the androgen pathway instead.
This happens developmentally causing masculinisation to varying extents of the external genitalia.
There are other intersex disorders mentioned.
La Chapelle Syndrome.
http://en.wikipedia.org/wiki/XX_male_syndromeThis is where an indivdual who is XX recives the SRY gene whitch is the "male factor" gene it gets stuck on the X chromosome by way of a mistaken crossover event... The X and the Y arn't supposed to crossover during meosis but because they are historically the same chromosome it can happen.
