A boy, 5, left, who identifies as a girl, plays with a friend in Northern California. He began emulating girls shortly after turning 3.

OAKLAND, Calif., Dec. 1 — Until recently, many children who did not conform to gender norms in their clothing or behavior and identified intensely with the opposite sex were steered to psychoanalysis or behavior modification.

But as advocates gain ground for what they call gender-identity rights, evidenced most recently by New York City’s decision to let people alter the sex listed on their birth certificates, a major change is taking place among schools and families. Children as young as 5 who display predispositions to dress like the opposite sex are being supported by a growing number of young parents, educators and mental health professionals.

Doctors, some of them from the top pediatric hospitals, have begun to advise families to let these children be “who they are” to foster a sense of security and self-esteem. They are motivated, in part, by the high incidence of depression, suicidal feelings and self-mutilation that has been common in past generations of transgender children. Legal trends suggest that schools are now required to respect parents’ decisions.

“First we became sensitive to two mommies and two daddies,” said Reynaldo Almeida, the director of the Aurora School, a progressive private school in Oakland. “Now it’s kids who come to school who aren’t gender typical.”

The supportive attitudes are far easier to find in traditionally tolerant areas of the country like San Francisco than in other parts, but even in those places there is fierce debate over how best to handle the children.

Cassandra Reese, a first-grade teacher outside Boston, recalled that fellow teachers were unnerved when a young boy showed up in a skirt. “They said, ‘This is not normal,’ and, ‘It’s the parents’ fault,’ ” Ms. Reese said. “They didn’t see children as sophisticated enough to verbalize their feelings.”

As their children head into adolescence, some parents are choosing to block puberty medically to buy time for them to figure out who they are — raising a host of ethical questions.

While these children are still relatively rare, doctors say the number of referrals is rising across the nation. Massachusetts, Minnesota, California, New Jersey and the District of Columbia have laws protecting the rights of transgender students, and some schools are engaged in a steep learning curve to dismantle gender stereotypes.

At the Park Day School in Oakland, teachers are taught a gender-neutral vocabulary and are urged to line up students by sneaker color rather than by gender. “We are careful not to create a situation where students are being boxed in,” said Tom Little, the school’s director. “We allow them to move back and forth until something feels right.”

For families, it can be a long, emotional adjustment. Shortly after her son’s third birthday, Pam B. and her husband, Joel, began a parental journey for which there was no map. It started when their son, J., began wearing oversized T-shirts and wrapping a towel around his head to emulate long, flowing hair. Then came his mothers’ silky undershirts. Half a year into preschool, J. started becoming agitated when asked to wear boys’ clothing.

En route to a mall with her son, Ms. B. had an epiphany: “It just clicked in me. I said, ‘You really want to wear a dress, don’t you?’ ”

Thus began what the B.’s, who asked their full names not be used to protect their son’s privacy, call “the reluctant path,” a behind-closed-doors struggle to come to terms with a gender-variant child — a spirited 5-year-old boy who, at least for now, strongly identifies as a girl, requests to be called “she” and asks to wear pigtails and pink jumpers to school.

Ms. B., 41, a lawyer, accepted the way her son defined himself after she and her husband consulted with a psychologist and observed his newfound comfort with his choice. But she feels the precarious nature of the day-to-day reality. “It’s hard to convey the relentlessness of it, she said, “every social encounter, every time you go out to eat, every day feeling like a balance between your kid’s self-esteem and protecting him from the hostile outside world.”

The prospect of cross-dressing kindergartners has sparked a deep philosophical divide among professionals over how best to counsel families. Is it healthier for families to follow the child’s lead, or to spare children potential humiliation and isolation by steering them toward accepting their biological gender until they are older?

Both sides in the debate underscore their concern for the profound vulnerability of such youngsters, symbolized by occurrences like the murder in 2002 of Gwen Araujo, a transgender teenager born as Eddie, southeast of Oakland.

“Parents now are looking for advice on how to make life reasonable for their kids — whether to allow cross-dressing in public, and how to protect them from the savagery of other children,” said Dr. Herbert Schreier, a psychiatrist with Children’s Hospital and Research Center in Oakland.

Dr. Schreier is one of a growing number of professionals who have begun to think of gender variance as a naturally occurring phenomenon rather than a disorder. “These kids are becoming more aware of how it is to be themselves,” he said.

In past generations, so-called sissy boys and tomboy girls were made to conform, based on the belief that their behaviors were largely products of dysfunctional homes.

Among the revisionists is Dr. Edgardo Menvielle, a child-adolescent psychiatrist at the Children’s National Medical Center in Washington who started a national outreach group for parents of gender-variant children in 1998 that now has more than 200 participants. “We know that sexually marginalized children have a higher rate of depression and suicide attempts,” Dr. Menvielle said. “The goal is for the child to be well adjusted, healthy and have good self-esteem. What’s not important is molding their gender.”

The literature on adults who are transgender was hardly consoling to one parent, a 42-year-old software consultant in Massachusetts and the father of a gender-variant third grader. “You’re trudging through this tragic, horrible stuff and realizing not a single person was accepted and understood as a child,” he said. “You read it and think, O.K., best to avoid that. But as a parent you’re in this complete terra incognita.”

The biological underpinnings of gender identity, much like sexual orientation, remain something of a mystery, though many researchers suspect it is linked with hormone exposure in the developing fetus.

Studies suggest that most boys with gender variance early in childhood grow up to be gay, and about a quarter heterosexual, Dr. Menvielle said. Only a small fraction grow up to identify as transgender.

Girls with gender-variant behavior, who have been studied less, voice extreme unhappiness about being a girl and talk about wanting to have male anatomy. But research has thus far suggested that most wind up as heterosexual women.

Although many children role-play involving gender, Dr. Menvielle said, “the key question is how intense and persistent the behavior is,” especially if they show extreme distress.

Dr. Robin Dea, the director of regional mental health for Kaiser Permanente in Northern California, said: “Our gender identity is something we feel in our soul. But it is also a continuum, and it evolves.”

Dr. Dea works with four or five children under the age of 15 who are essentially living as the opposite sex. “They are much happier, and their grades are up,” she said. “I’m waiting for the study that says supporting these children is negative.”

But Dr. Kenneth Zucker, a psychologist and head of the gender-identity service at the Center for Addiction and Mental Health in Toronto, disagrees with the “free to be” approach with young children and cross-dressing in public. Over the past 30 years, Dr. Zucker has treated about 500 preadolescent gender-variant children. In his studies, 80 percent grow out of the behavior, but 15 percent to 20 percent continue to be distressed about their gender and may ultimately change their sex.

Dr. Kenneth Zucker, a psychologist at the Center for Addiction and Mental Health in Toronto, encourages children to be content with their gender.

Dr. Zucker tries to “help these kids be more content in their biological gender” until they are older and can determine their sexual identity — accomplished, he said, by encouraging same-sex friendships and activities like board games that move beyond strict gender roles. Though she has not encountered such a situation, Jennifer Schwartz, assistant principal of Chatham Elementary School outside Springfield, Ill., said that allowing a child to express gender differences “would be very difficult to pull off” there.

Ms. Schwartz added: “I’m not sure it’s worth the damage it could cause the child, with all the prejudices and parents possibly protesting. I’m not sure a child that age is ready to make that kind of decision.”

The B.’s thought long and hard about what they had observed in their son. They have carefully choreographed his life, monitoring new playmates, selecting a compatible school, finding sympathetic parents in a babysitting co-op. Nevertheless, Ms. B. said, “there is still the stomach-clenching fear for your kid.”

It is indeed heartbreaking to hear a child say, as J. did recently, “It feels like a nightmare I’m a boy.”

The adjustment has been gradual for Mr. B., a 43-year-old public school administrator who is trying to stop calling J. “our little man.” He thinks of his son as a positive, resilient person, and his love and admiration show. “The truth is, is any parent going to choose this for their kid?” he said. “It’s who your kid is.”

Families are caught in the undertow of conflicting approaches. One suburban Chicago mother, who did not want to be identified, said in a telephone interview that she was drawing the line on dress and trying to provide “boy opportunities” for her 6-year-old son. “But we can’t make everything a power struggle,” she said. “It gets exhausting.”

She worries about him becoming a social outcast. “Why does your brother like girl things?” friends of her 10-year-old ask. The answer is always, “I don’t know.”

Nila Marrone, a retired linguistics professor at the University of Connecticut who consults with parents and schools, recalled an incident last year at a Bronx elementary school in which an 8-year-old boy perceived as effeminate was thrown into a large trash bin by a group of boys. The principal, she said, “suggested to the mother that she was to blame, for not having taught her son how to be tough enough.”

But the tide is turning.

The Los Angeles Unified School District, for instance, requires that students be addressed with “a name and pronoun that corresponds to the gender identity.” It also asks schools to provide a locker room or changing area that corresponds to a student’s chosen gender.

One of the most controversial issues concerns the use of “blockers,” hormones used to delay the onset of puberty in cases where it could be psychologically devastating (for instance, a girl who identifies as a boy might slice her wrists when she gets her period). Some doctors disapprove of blockers, arguing that only at puberty does an individual fully appreciate their gender identity.

Catherine Tuerk, a nurse-psychotherapist at the children’s hospital in Washington and the mother of a gender-variant child in the 1970s, says parents are still left to find their own way. She recalls how therapists urged her to steer her son into psychoanalysis and “hypermasculine activities” like karate. She said she and her husband became “gender cops.”

“It was always, ‘You’re not kicking the ball hard enough,’ ” she said.

Ms. Tuerk’s son, now 30, is gay and a father, and her own thinking has evolved since she was a young parent. “People are beginning to understand this seems to be something that happens,” she said. “But there was a whole lifetime of feeling we could never leave him alone.”