At the age of 6 months, the baby had surgery to reduce the size of her clitoris and open her labia. She'll need another one at puberty to widen the vaginal canal.
Wu said doctors no longer use a surgical technique that pulls the clitoris under the pubic bone, which can cause painful orgasms in adulthood. He uses a nerve-sparing technique that removes the erectile portion of the clitoris.
"In this kind of case, she didn't fit into the typical DSD classification and it made it challenging," he said. "We try to predict what the gender identity will be, and three or four years later, the child psychologist can give us some kind of idea."
Parents are also confused. "It's so hard to accept that my child will look different to anyone who changes the diapers," said Wu. "Some parents are so torn by the fear that they will make the wrong choice and mess up the child forever."
Hormones are identical in children until they reach puberty, but by the time they are about 12 their bodies can change.
"The thing we worry about is if something starts to kick in when they age and they are not the sex we raised the child," he said. "What do we do then?"
Anne Tamar-Mattis, executive director of Advocates for Informed Choice, worries about the legal side of this complicated issue, especially when it involves sterilization without a child's consent.
"We don't weigh in on what medical decisions people should make," she said. "We weigh in on children's rights. If the decision involves sterilization, the child has a right to court over sight."
And when parents are making these complex decisions to remove the child's reproductive organs, they must be fully informed. Often, they are not, she said.
Katrina Karkazis, senior research scholar at Stanford's Center for Biomedical Ethics and author of "Fixing Sex: Intersex, Medical Authority and Lived Experience," agrees that "the child can't speak for him or herself."
The American Academy of Pediatrics' Consensus of Care was established in 2006 to address treatment of intersex disorders.
"Everyone agrees there must be gender assignment," she said. "In a good scenario, the physician makes a decision with a lot of reflection and without rushing in to anything and in consult with the parents."
The number of children who don't accept their gender assignment is small, according to Karkazis. "What's missing is these families and kids don't get the appropriate social and psychological support."
She recommends that doctors "check in" with the child over his or her life span and "find out what they are feeling."
Behavior is not always the best indicator.
"Pay attention to what child a child is telling you -- there may be a switch which needs to be evaluated with expertise," she said. "Plenty of kids go through phases -- I am a girl or I am a boy -- and it ends after a year. But one thing that is irreversible is surgery."
"Once you've removed the tissues, you can't put them back," she said. "It's infinitely more complicated and for the most part, you cannot replace a phallus."