The transition is so common the children are referred to as Guevedoces, or `penis at 12 years`.
Johnny is one of the babies affected and was initially brought up as a girl named Felicity by his parents.
The 24-year-old said doctors didn`t originally know what sex he was but he always felt more like a boy, according to the BBC.
He said: `I went to school and I used to wear my skirt. I never liked to dress as a girl.
`When they bought me girls` toys I never bothered playing with them - when I saw a group of boys I would stop to play ball with them.`
Another boy, named Carla, said he is also going through the same transition aged nine after appearing to be born a girl.
Pictures show Carla, who will change his name to Carlos, wearing a pink patterned top with his hair in bunches as he smiles alongside his cousin Catherine.
The condition was first discovered in the 1970s after a scientist from Cornell visited the island.
Babies usually form male sex organs after around eight weeks in the womb, with the change triggered by hormone dihydro-testosterone.
But a handful of babies do not have the enzyme that triggers the hormone surge and consequently appear to be born female.
They will not form male genitalia until they reach puberty, when there is another surge of testosterone.
Some experts have suggested there is such a high concentration of children affected in Salinas due to the village`s isolation.
The extraordinary condition will be explored by Dr Michael Mosley on BBC Two`s Countdown to Life - The Extraordinary Making of You tomorrow night.
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