IN MANY WAYS, Avery Jackson seems like a typical nine-year-old girl. Spunky and confident, she likes reading, gymnastics, playing with friends, and all things pink, purple or sparkly. Yet Avery was born biologically male. “At the age of four, she told us, ‘You think I’m a boy, but I’m a girl on the inside,’ ” says her mother, Debi Jackson.

As a preschooler, Avery had preferred playing with dolls and dressing up with the girls in her class. That kind of cross-gender play is common for young children. But Avery didn’t grow out of it, and when Debi tried to discourage Avery’s behavior, it became obvious she wasn’t confused or playing make-believe. “She wanted to wear a dress all the time at home, sleep in nightgowns, go out on weekends dressed as a girl—she called it ‘me’ time,” says Jackson.

Within a year of telling her mother, Avery began to grow angry and depressed, and to show an aversion to her male sexual anatomy. The Jacksons took Avery to a pediatrician, to a child psychologist and eventually to a local gender therapist. The therapist helped them understand that their young child probably was transgender—that the gender she identified with was at odds with her biological sex. And while being transgender is no longer considered a psychological disorder, Avery’s growing distress over the mismatch between the body she had been born with and the gender she considered hers led the specialist to diagnose her condition as gender dysphoria.

“We didn’t know anything about what that was,” says Jackson, but she and her husband began to read what little they could find about the condition. They decided to follow the therapist’s advice—to let Avery live publicly as a girl, exploring her perceived gender identity before she reached puberty. Since then, Avery and her family have appeared across news media, advocating for transgender awareness.

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THE ISSUES THAT THE JACKSONS and Avery face are at the center of a widening discussion among families, physicians and other caregivers about the proper course of treatment for children who don’t identify with their biological sex. At least until recently, kids in that situation often were prescribed antidepressants or other medications, and even today, some are sent for “conversion therapy,” a discredited process that, among other aims, attempts to bring gender identity and expression in line with biological sex.

In 2013, the American Psychiatric Association stopped describing gender variance as a disorder in its manuals, and several states have banned conversion therapy. “Gender variance isn’t pathological; it’s not something to be overcome or cured,” says Diane Ehrensaft, a clinical psychologist and director of mental health at the Child and Adolescent Gender Center at University of California, San Francisco Benioff Children’s Hospital.

Yet for the parents and physicians of these children who may not identify with their birth sex, there’s still scant consensus on what to do or not to do. There is little reliable research about what causes gender variance, how prevalent it is, or even how to determine what gender struggles a particular child is going through. “Kids are the ones who tell us about their gender identity, and we have to listen to them,” says Ehrensaft.

A major complication is that children with gender issues face a diverging path. Many outgrow their cross-gender feelings entirely, making it unnecessary and unwise to treat them pharmacologically for a condition that may not persist. But for those for whom it does persist, gender dysphoria may intensify, particularly as they begin to experience an unwanted biological puberty. Not treating those kids is also dangerous.

In the past, children at this crossroads had no choice but to see their puberty through. Today, however, a small but growing number of young children and adolescents are discovering other options, up to and including medical and even surgical gender reassignment. “There has been very rapid growth in younger patients looking to affirm their opposite sex,” says Norman Spack, a pediatric endocrinologist and co-director and co-founder emeritus of the Gender Management Service (GeMS) program at Boston Children’s Hospital, the first U.S. transgender youth treatment clinic, which opened in 2007.

Still, there are few experienced practitioners or standard protocols for any of this, and insurance coverage is a problem. Moreover, there’s growing debate about when or whether to tamper with the bodies of otherwise healthy children. Offering gender reassignment therapies to minors can have physical consequences, including sterility. Some clinicians adamantly oppose giving hormones or other treatments to kids who identify as transgender.

“I am increasingly being contacted by mental health professionals, primary care providers, surgeons and even ob-gyns who are horrified by the conditioning of children into a life of chemical and surgical impersonation of the opposite sex and all the suffering that entails,” says Michelle Cretella, a pediatrician and president of the American College of Pediatricians in Gainesville, Fla., a socially conservative organization with 500 physician members. (The American Academy of Pediatrics, with 64,000 physician members, is on the other hand supportive of hormonal transition when appropriate for transgender youth.)

But many who counsel and treat transgender children see things differently. “Lots of people disagree with the work we’re doing, but in my experience, it’s lifesaving,” says Stephen Rosenthal, a pediatric endocrinologist and medical director at UCSF’s Child and Adolescent Gender Center.

“WE DON’T KNOW WHY anyone is the gender they are,” says Johanna Olson-Kennedy, a pediatrician and medical director at the Center for Transyouth Health and Development at Children’s Hospital Los Angeles. Research suggests that by the age of three most children have a sense of what it means to be male or female, and by five or six, they have identified with one gender or the other. Most often, that aligns with their biological sex and will stay that way for life.

But in rare cases—involving one in 10,000 biological males and one in 30,000 biological females, according to an estimate by the American Psychological Association—sex and gender don’t align, and that can cause a range of problems. Yet while surveys suggest that two out of three transgender adults experienced gender dysphoria during childhood, making that diagnosis for children is problematic. Kids’ gender identities can fluctuate, and symptoms of gender dysphoria diminish or disappear by puberty for a large percentage of children—perhaps because of hormonal changes, peer pressure or cognitive development.

Still, it is almost impossible to generalize about the psychological development of gender, in large part because there’s so little reliable research. Most studies have involved small samples and many were conducted years ago, when gender variance was still regarded as a disorder by the APA.

Among the few studies considered valuable is a 2013 one that aimed to identify factors associated with the persistence of gender dysphoria into adolescence. Researchers followed 127 kids diagnosed with the condition in childhood for four years, and found that persistence of dysphoria was greater among biological females. Persisters also reported more body dissatisfaction and a higher incidence of same-sex sexual orientation. In another small but important study, published last year, researchers determined that most transgender children are certain of their gender identity on a deep level. The University of Washington study involved 32 children, ages 5 to 12, who identified as transgender; they were compared with two control groups of “cisgender” children, whose gender identities matched their birth sex.

Participants in each group answered questions about their gender identity and took the Implicit Association Test, which measures the speed with which they associate male and female genders with concepts of “me” and “not me.” Transgender participants scored as strongly with their cross-gender identity as the kids in the two control groups scored with their biological gender, which the researchers took as evidence that their identities are deeply held and consistent, and not the result of confusion or fantasy.

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What hasn’t been found, however, are any measurable biological indicators—biomarkers—that could help confirm a child’s transgenderism. A recent study published in the Journal of Adolescent Health ruled out circulating hormone levels. Looking at 101 transgender participants ages 12 to 24, the researchers discovered that the young people’s hormone levels were in line with those of others of the same biological sex, regardless of gender identity.

Olson-Kennedy says she was struck by another finding—that while participants, on average, were eight years old when they recognized that their gender was different from their assigned sex at birth, they were 17 before they told their families. “That’s a really critical period of brain development, and if that’s happening while you’re sitting on a core secret about yourself, and internalizing the message that your authentic self isn’t okay, that’s going to have consequences that we don’t know much about yet,” she says. And living with that secret has a negative impact on mental health, the study confirmed. More than a third of participants experienced depression; more than half said they’d considered suicide, and nearly a third reported making at least one attempt.

BECAUSE MOST FAMILY PHYSICIANS and pediatricians consider transgender care outside of their expertise, children and their families seeking help tend to be referred to clinics or networks of specialists—where the wait for an appointment can stretch to many months. “We have patients coming from throughout New England and along the East Coast,” says Michelle Forcier, a pediatrician at a clinic in Hasbro Children’s Hospital in Providence, R.I. Forcier created the clinic, the only one in the state, in 2011, and today she treats 300 gender-variant patients.

Patients at such specialty clinics typically undergo extensive screening and psychotherapy to determine whether they have gender dysphoria. “We’ve developed a 23-page gender assessment packet that includes interview tools as well as observation and play techniques to learn about the child’s gender development,” says UCSF’s Diane Ehrensaft.The goal is to find out which kids are most likely to continue to identify with a different gender than the one they were born with.

As kids move closer to puberty, discussions center on what patients and their families want to do. There could be “social transitions” involving a change in clothing and hairstyle or assuming a new name or gender pronoun. Yet such changes may do little to dispel the terror many adolescents feel about the prospect of unwanted changes to their bodies. And behavioral problems, including self-mutilation and suicide attempts, tend to escalate as puberty approaches.

Treatment with puberty-blocking drugs, pioneered in the Netherlands and endorsed in 2009 by the U.S. Endocrine Society, can buy time, stopping the pituitary gland from sending hormones to stimulate the ovaries and testes to produce estrogen and testosterone. For transgender children, such treatments can have dramatic results, reducing gender dysphoria and improving social and academic performance. They may also help kids avoid future surgery; no mastectomy will be needed, for example, if a transgender male never develops breasts.

Among the possible risks of such treatment, which can affect bone density, are potential hazards to brain development, a process that continues until the mid-twenties. But in a study of several dozen adolescents published last year, Dutch researchers found no significant effects of the drugs on brain regions associated with “executive functioning” skills, which affect the ability to plan, focus attention, remember instructions and handle several tasks at once. And other evidence suggests that puberty-blocking drugs, which have been used for years to delay puberty when it comes too early, are safe and reversible. If the medications are discontinued, a normal puberty will begin.

AFTER TAKING PUBERTY BLOCKERS for several years, adolescents who choose to continue their cross-gender transition move to the next step: Instead of blocking the hormones that would bring on puberty, they begin taking those associated with the gender they identify with. Transgender females receive estrogen, the feminizing hormone that spurs breast development, the redistribution of body fat and wider hips. Transgender males get testosterone, which causes voice pitch to drop, facial and body hair to grow and shoulders to get broader. The Endocrine Society guidelines call for waiting until age 16 to start these medications, but physicians may prescribe them to children as young as 13—and clinicians say their experience in this relatively new frontier is teaching them that waiting too long may be harmful, putting transgender teens out of step with the physical development of their cisgender peers.

There are many unanswered questions about the possible health risks of cross-sex hormone therapy, in part because this generation of transgender youth is the first to start what will be lifelong treatment. Research suggests that taking estrogen puts transgender females at a higher risk for blood clots, while transgender males taking testosterone could be subject to increased hemoglobin levels and high cholesterol, among other side effects. New data from a large study of 1,000 adults has also shown that transgender females on hormone therapy have elevated risks of heart disease.

That study, published in the European Journal of Endocrinology, also showed that transgender female adults in the Netherlands tended to die earlier than cisgender males, with above-average rates of suicide, AIDS and drug abuse. Mortality rates for transgender males, however, were in line with those of the general female population.

With such risks looming, Michelle Cretella of the American College of Pediatricians calls “affirming gender discordance” and its treatments that help children transition to a new gender “institutionalized child abuse at the hands of professionals.” Other critics also say they are concerned that children are being coerced into gender reassignment therapies. Yet Spack sees a very different dynamic at work, with parents and kids grappling with all of the implications of what is an extremely difficult decision. “No one chooses this for themselves or for their child,” he says.

Research has shown that about one in 50 transgender adults regrets his or her transition, and that ratio could be even lower for young people now going through that process at an earlier age, who spend more of their life in the gender they identify with. A small Dutch study, published in 2014, followed 55 transgender people receiving treatment from youth to early adulthood. All had been diagnosed with gender dysphoria and received puberty blockers and then cross-sex hormones. Surveyed at the average age of 21, they reported they were no longer experiencing gender dysphoria, their quality of life and happiness levels were found to be at least as high as those of their cisgender peers, and none expressed any regret about delaying puberty or transitioning to the gender they identified with. Considering the high rates of depression and suicide of transgender youth who had not received any treatment, the study is a powerful argument for acting early.

MORE DEFINITIVE ANSWERS about the long-term effects of medical treatments for transgender youth could come from a new $5.7 million five-year study funded by the National Institutes of Health. Four academic medical centers will enroll 280 kids with gender dysphoria and look at the safety and effectiveness of treatments, including use of hormone blockers and cross-sex hormones.

Results of that study could help shape future care of transgender youth, which today continues to be based largely on expert opinion and experience rather than on conclusive scientific data. “Everything about transgenderism is pretty much conjecture,” says Spack, who has been delivering transgender care since the late 1990s. “The most important thing we know is how much more we need to know.”

The willingness of health insurers to pay for any kind of transgender care also remains a work in progress. In 2009, only 49 major U.S. employers offered such coverage, but by 2016 that number had increased to 511, according to the Corporate Equality Index from the Human Rights Campaign Foundation. Yet only a handful of states have expanded Medicaid benefits to include mental health treatment, hormone therapy and sexual reassignment surgery for adults. Even fewer pay for children to receive puberty-suppressing drugs, which haven’t been approved by the Food and Drug Administration for use in the transgender population. Such treatment may cost as much as $30,000 annually—an insurmountable hurdle for many who would have to pay for therapy out of pocket.

Indeed, Debi Jackson and her husband are among increasing numbers of parents who consider the high cost of care essential to ensure their children’s welfare. “We’ve been saving money for Avery for quite a while,” says Jackson. If Avery’s gender dysphoria persists, which they feel is likely, the Jacksons are comfortable with having Avery receive puberty blockers and cross-hormone treatments. Debi Jackson says: “We have a retirement account, a college account and a gender account, because we know our health insurance isn’t going to cover Avery’s care.”