“This is the first time we’ve had a federal government report of this magnitude showing that transgender youth exist in this country and in larger numbers than researchers had previously estimated,” he said in an interview. The report, he said, shows “the very real health risks” transgender youth face in school.

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Paley said the Trump administration has moved to “erase the identity of transgender youth.” The administration has rolled back or frozen Obama-era anti-discrimination rules aimed at protecting the LGBTQ community in health, education and other areas.

The Supreme Court on Tuesday allowed President Trump’s broad restrictions on transgender people serving in the military to go into effect while the policy is fought in lower courts. In 2017, Education Secretary Betsy DeVos’s first major policy act was to support Trump’s decision to rescind the guidance protecting the right of transgender students to use the bathroom of their choice.

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The data published by the CDC comes from the 2017 Youth Risk Behavior Survey in 10 states and nine large urban school districts. The survey is conducted biennially among a representative sample of U.S. high school students in the ninth through 12th grades. The findings were published in the CDC’s Morbidity and Mortality Weekly Report, an epidemiological digest with public health information and recommendations sent to the CDC by state health departments.

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In 2017, 10 states and nine urban school districts piloted a measure of transgender identity. The states were Colorado, Delaware, Hawaii, Maine, Maryland, Massachusetts, Michigan, Rhode Island, Vermont and Wisconsin. The urban school districts included Boston, Cleveland, Detroit, the District, Los Angeles, New York, San Diego, San Francisco and Broward County, Fla.

The CDC said it pooled data from the 19 sites to assess the prevalence of transgender identity and the relationship between transgender identity and violence victimization, substance use, suicide risk and sexual risk behaviors. Transgender students were more likely to report substance use, suicide risk and being victims of violence, and, although more likely to report some sexual risk behaviors, they were also more likely to be tested for HIV infection, the CDC said.

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“These findings indicate a need for intervention efforts to improve health outcomes among transgender youths,” the report said.

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Across the 19 sites, 94.4 percent of students responded, “No, I am not transgender”; 1.8 percent responded, “Yes, I am transgender”; 1.6 percent responded, “I am not sure if I am transgender”; and 2.1 percent responded “I do not know what this question is asking.”

It has been difficult for health experts to determine the percentages of young people who identify as transgender or gender-nonconforming, and estimates have varied in recent years depending on the survey.

A 2018 report in the journal Pediatrics used a statewide survey of nearly 81,000 Minnesota ninth- and 11th-graders and found that nearly 3 percent identified as transgender or gender-nonconforming, meaning they do not identify as the gender they were assigned at birth. The authors of the study said their findings could be used to estimate numbers in those grades across the country.