This is how the gender identity counselor explained it to Elsa and her sibling during family sessions.

“You are talking about how you feel inside. Others are talking about your body. Those are two different things.”

It was up to Elsa, the counselor said, to decide who she was.

Gender identity, a psychological sense of self as male or female, isn’t something most people think about. It’s just there, part of the inner voice. But for those who are transgender, an estimated three in 1,000 people according to a 2011 University of California at Los Angeles study, that inner voice is in conflict.

This can start as early as 18 months old.

“Once upon a time we didn’t call this anything. It was invisible,” said Dr. Sarah Burgamy, a Denver clinical psychologist and gender identity specialist.

“Gender identity disorder” first appeared in the Diagnostic and Statistical Manual of Mental Disorders in 1980. The latest version of the manual, in 2013, renamed it “gender dysphoria,” removing the stigma of a “disorder” but still recognizing mental health problems caused when someone “whose gender at birth is contrary to the one they identify with.”

Among psychologists, there is a growing sense that gender dysphoria isn’t an indication that “something is wrong,” just a “variation on human identity,” Burgamy said. Parents who seek her help always want answers to two questions: “What caused it?” and “Did I cause it?”

Her answer to both: gender identity develops on its own. Society looks at only one part of the equation when assigning gender — what’s between a person’s legs. There is no scientific test for whether a person feels male or female.

Among gender identity specialists, the growing sentiment is that counseling to push a child to conform to their assigned gender doesn’t work, although some parents seek that type of treatment. Many gender experts say parents should give children room to explore their gender identity without pushing them in a certain direction. If given space, they will discover what is innate.

A few decades ago, common medical thought was that parents could “socialize” gender. The infamous “John-Joan” case of 1965, about a baby whose circumcision went horrifically wrong, is referenced as proof that raising a child as a certain gender cannot override gender identity.

When the penis of one of two Canadian identical twins was nearly burned off, a doctor at Johns Hopkins Hospital recommended surgery to create female anatomy. The baby’s parents were advised to raise him as female. The boy suffered a life of misery because he never felt like a girl, despite pretty dresses and injections of female hormones, and by age 13, was suicidal, according to a book about his life. He transitioned to a male at age 14 after learning what had happened to him.

He killed himself at 38.

The case, which wasn’t widely known until the late 1990s, has shaped how doctors advise parents of children born intersex, with genitalia neither clearly male nor female. About one in 2,000 infants are born intersex, including some who have an extra sex chromosome, beyond the typical XX or XY.

“Things can happen or perhaps they just are,” said Anna Wegleitner, a highly sought Denver family physician who saw her first transgender patient 23 years ago. She now has a waiting list months long and accepts only transgender patients, seeing two to three new ones per day. “I tend to think it’s part of the human experience. People want to know why because they want to be able to fix it.”