Charlie was just three years old, sitting in the tub at bath time, when he looked up at his mom and asked: “Will my penis ever disappear? When will it shrink?”

It was a pivotal moment for the family — and the beginning of a journey that would see Charlie the boy transition into Charlie the girl.

“I was a little bit panicked, as you can imagine,” recalls Charlie’s mother, Anne Lowthian. “It was one of those deer-in-the-headlights moments for parents because you go: ‘How do I answer that?”‘

“So I looked at Charlie and said: “Is that what you want?’ And she said, ‘Yes, because I’m a girl.'”

It wasn’t the first time her son had embraced the traditionally feminine. By age two, his favourite colour was pink. By three, “Mamma Mia” was his most beloved movie and he wanted to dress up in heels and have fairy wings. But Charlie also loved cars, and was a whiz at that so-called boy thing, memorizing every make and model on the road.

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As a teacher, Lowthian knew that children that age often try on different roles, so she and husband Chris Rickert didn’t see it as a big deal.

Charlie’s bathtub avowal changed all that. “We realized this wasn’t a passing thing. This was not a phase. This was a part of who she was.”

“Chris and I talked about it. We were concerned, because we thought what’s this going to mean for her if she truly identifies as a girl? We had no experience with transgender, we had no idea what it was.”

A TV documentary on transgender children and Internet searches filled in a lot of the blanks for the couple, who also took Charlie to the Gender Diversity Clinic at the Children’s Hospital of Eastern Ontario, or CHEO, in Ottawa.

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Believing it was important for their child to freely express himself, they didn’t blink when Charlie, age 4, went to preschool in their rural eastern Ontario community dressed as a boy, but wearing nail polish and pink and purple clothes. He told teachers he was really a girl.

It wasn’t well-accepted.

Charlie, age 9, was born as a male but identifies as a female. THE CANADIAN PRESS/Sean Kilpatrick

“They ostracized her,” Lowthian says of school administrators. “They made her eat lunch alone. Even in line-ups in a hallway, she had to line up on the other side of the hallway.”

And then there was the bullying by other kids.

“They hurt me physically and verbally,” says Charlie, now 9. “They’d give me noogies, they’d punch me, they’d bite me. They called me names. They started calling me ‘girlish boy.”‘

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WATCH: 16×9 feature on two transgender children struggling to be themselves

The family, who lost long-time friends over their decision not to make their child “conform,” moved to Ottawa and found a supportive school for Charlie, who entered Grade 1 living full-time as a girl.

“Oh my goodness, it was wonderful to watch,” says Lowthian. “You’ve never heard a girl squeal with delight like Charlie did when she got her first princess dress, and then all the dresses after that. And how much fun is it to go shopping with a child who is so thrilled to be looking in the mirror at a person they actually like and feel comfortable with.

“To see her get up and go to school every day confident in who she was and happy to be who she was, it was just thrilling.” Tweet This

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READ MORE: Alberta gives new birth certificate to transgender boy who was born a girl

Until recently, a mismatch between biological sex and gender identity had been deemed a mental disorder in the psychiatric bible known as the Diagnostic and Statistical Manual. But the latest version, the DSM-5, renamed the phenomenon gender dysphoria, defined as a persistent conflict and discomfort with one’s biological sex.

There are no solid statistics on how many children and adults feel their inner gender is at odds with their physical sex, but worldwide estimates range from one in 200 to one in 500.

Those figures don’t surprise Dr. Stephen Feder, head of CHEO’s Gender Diversity Clinic, which last year saw 40 to 50 gender-nonconforming children and teens with their families.

Doctors spend time getting to know the child or youth and listening to their experiences, as well as obtaining corroborating information from parents. They also look for mental health issues, such as depression or drug use, which might affect how a young person presents their gender, and try to determine the child’s ability to make a sound decision.

“Just because a child at six or seven or eight identifies as gender nonconforming doesn’t mean that they’ll necessarily maintain that at puberty,” says Feder.

One study suggests that three-quarters of children who present as the opposite gender later revert back, though it’s a figure he tends to take “with a grain of salt” because the reasons can be many and varied, including the fact that life in a transphobic society can be daunting, even dangerous.

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WATCH: Fighting for transgendered children and youth’s rights

“But that said, we’re talking about the kid in the moment, not the kid four years from now. So the issue is how do you support that child where they are now. And you do that as you would for any child, by trying to support them 100 per cent: love them, care for them, nurture them, praise them, and really try to bolster their self-esteem.”

The Gender Identity Clinic for children at the Centre for Addiction and Mental Health in Toronto goes through a similar assessment, but the primary aim is to reduce anxiety or depression in young patients who question their gender and to ease any distress parents might feel, especially if bullying has been an issue.

In some cases, that may mean suggesting that a child avoid cross-gender attire and activities, to see if he or she becomes more comfortable with their biological sex over time, says Dr. Kwame McKenzie, the medical director overseeing the clinic.

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While some parents see that as practical advice, others view it as trying to change someone’s expressed gender identity, he says, leading to accusations that clinic staff are practising “reparative” or “conversion” therapy.

It’s a claim McKenzie vehemently denies.

“The overall aim is to decrease mental health problems in young distressed kids … The aim is not to redirect or change somebody’s gender identity.”

Still, with a firestorm brewing within the transgender community – including an online petition calling for clinic head Dr. Kenneth Zucker to be sacked – CAMH in February announced an external review of the service, based on concerns brought forth by the LGBTQ organization Rainbow Health Ontario. A report is expected this summer.

WATCH: NDP wants to end ‘conversion therapy’ for children with gender identity questions

Meanwhile, Ontario NDP MPP Cheri Dinovo tabled a bill that would ban reparative therapy for sexual orientation or gender identity in those 18 and under and delist it as an insured service for adults. Bill 77 passed second reading April 2 and was sent to committee for further discussion.

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The issue is also making headlines south of the border: last week, President Barack Obama signalled support for measures that would abolish psychiatric therapy sessions seeking to change the sexual orientation of young people.

READ MORE: Obama looks to end LGBTQ ‘conversion therapy’, still legal in Canada

Dinovo’s proposed legislation was inspired by the suicide of Ohio transgender teen Leelah Alcorn, 17, who walked to her death in front of a tractor-trailer in December. Her suicide note explained that her parents had rejected her, then taken her for corrective therapy. Alcorn’s final words were: “Fix society. Please.”

While some young children’s gender identity may be more fluid, that doesn’t seem to be the case for adolescents: about 80 per cent of those who identify as the opposite gender after puberty will remain transgender as adults.

Elizabeth’s daughter knew by 16 that she was meant to be male – and the disconnect between her inner self and her body was leaving her depressed, anxious and sometimes suicidal.

She left a letter in the bathroom for her mother to find, then went to school.

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“The letter was defining what he hated about his body and that he really didn’t want that on him, talking about the breasts especially, and that he … she … felt he was a guy, not a girl,” says Elizabeth.

“We spoke about it that night. I still didn’t believe in it. I knew something was wrong, but you never think about that.”

But over time and following assessment of her child by psychiatrists who specialize in gender diversity, as well as support from the parents group Gender Creative Kids, Elizabeth came to accept that she now had a son.

Between high school and college, the Montreal-area adolescent began dressing and presenting as male, calling himself Philippe (both he and his mother have been given pseudonyms to protect their identities).

“I was looking forward to transitioning because I was not happy about my life,” says Philippe, 19, who nevertheless worried about others’ reactions: “Was I going to still have some friends? Is my mom still going to love me?”

The teen took an estrogen-blocking drug to arrest further female sexual development, then began testosterone at 18 to develop male characteristics, such as increased body hair and bulkier muscles.

“And the first time he called me on the phone, the voice!” says his mom. “I thought,’ Oh, my God, it’s so deep.’ And he doesn’t look at all like he used to. He really looks like a guy now.

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“It’s hard. I have a lot of pictures of him when he was a girl, and he doesn’t want people that he now knows to see these pictures,” says Elizabeth. “I had to explain to him many times you can’t erase 17 years out of life. That was a beautiful 17 years and I remember.”

Despite their close bond and her unwavering support, she admits to feelings of loss.

“You feel like you’ve buried a daughter. And there are so many things that come with that: I’ll never go shopping for a wedding dress with him.” Tweet This

And there will be no biological grandchildren.

That said, her teen is more content and settled, and that’s reflected in higher marks at school, observes Elizabeth, and that makes her happy.

“I saw such a big difference in his well-being, his humour, how he felt,” she says. “He is a changed kid.”

For Charlie, not yet in puberty, decisions about whether to physically transition are still in the future.

Charlie, age 9, was born as a male but identifies as a female. THE CANADIAN PRESS/Sean Kilpatrick

That may mean taking puberty blockers, which will buy some time, “so that when she is 16, 17, 18, she can make more a permanent decision about the trajectory of her life and her identity, so she can find out for herself where her heart’s desire might be,” says her mother.

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“She may choose sex-reassignment surgery or she may not. Whatever she chooses, we’re going to support her.”

To Charlie, it’s all pretty simple.

“As a boy, I felt like I was trapped inside a body that I couldn’t get out of.”

“But now, since I’m able to be a girl, I’m very happy … I may have the body of a boy, but I have the heart and soul of a girl.”