Pentagon Reportedly Using Medical Records to Identify Transgender Troops

The Pentagon is using military medical and personnel records to identify service members with current or past diagnoses of gender dysphoria as it moves to separate transgender troops under the Trump administration’s ban, according to a Federal News Network investigation published Monday.

The effort has led commanders across the military to receive notices identifying troops in their units who may fall under the policy and directing them to begin the separation process, per the report. The outlet cited multiple service members, advocates and internal military documents.

An internal Air Force email obtained by Federal News Network said the Office of the Secretary of Defense had identified service members “who may have a current diagnosis or history of or exhibit symptoms consistent with gender dysphoria in their electronic healthcare record.”

The Pentagon, Defense Health Agency and individual military services declined to answer Federal News Network’s questions about the process, citing ongoing litigation.

The Pentagon did not immediately respond to Military.com’s request for comment on Monday.

The latest reporting offers a clearer picture of how the Pentagon is identifying service members who did not voluntarily come forward after the department began implementing its transgender service ban last year.

How the Pentagon Is Identifying Service Members

Defense officials have previously acknowledged that medical information would play a role in identifying troops subject to separation.

In May 2025, a senior defense official said the Individual Medical Readiness program would be the “primary means” of determining whether service members meet the new medical standards.

Under the policy, troops with a current diagnosis or history of gender dysphoria—or symptoms consistent with the condition—are generally disqualified from continued military service unless they receive a waiver.

The Pentagon estimated in May 2025 that roughly 4,200 service members had been diagnosed with gender dysphoria, though officials acknowledged the figure could have changed.

Defense officials said at the time that commanders who were already aware of a service member who met the criteria could direct an individualized review of that person’s medical records. The department also said troops would be evaluated through routine health screenings as they cycled through annual medical readiness requirements.

But Federal News Network’s reporting indicates identification is also occurring at higher levels of the Pentagon, reaching commanders through information contained in electronic medical records.

Sources who spoke with the outlet claim officials are using MHS Genesis, the Pentagon’s electronic health record system, as well as other military databases.

MHS Genesis supports more than 9.5 million military health system beneficiaries, including service members, military retirees and family members, and is designed to provide a single electronic health record across military care.

It was reported that one separation referral sent to an airman’s commander included information about the service member’s previous treatment, including counseling and medication.

The airman told the outlet they were not currently experiencing gender dysphoria and had not disclosed their past treatment to colleagues.

What Military Medical Privacy Rules Allow

The reported use of medical records raises questions about how much of a service member’s health information can be shared with commanders.

Military health information is generally protected by the Health Insurance Portability and Accountability Act, or HIPAA, but the law includes an exception for certain disclosures involving members of the armed forces.

Under what the Defense Health Agency calls the “Military Command Exception,” military health providers may disclose protected health information to command authorities for authorized activities, including determining fitness for duty, fitness to perform a particular assignment or other activities necessary to the military mission.

The exception does not give commanders unrestricted access to medical records.

The Defense Health Agency says health information disclosed under the command exception is no longer protected by HIPAA once provided to military command authorities, but remains protected under the Privacy Act of 1974.

Separate Defense Department rules generally restrict command notification when a service member receives mental health or substance abuse treatment unless certain circumstances apply, including a serious risk of harm to the service member, others or the military mission.

During a May 2025 Pentagon briefing, a senior defense official said commanders would be required to protect medical information received as part of the transgender separation policy.

The official also said the Pentagon remained “committed to protecting both their privacy and their medical data.”

An internal Army order issued in August explicitly limits how commanders themselves can search for affected soldiers. The order bars commanders from broadly searching health and personnel records for soldiers with gender dysphoria or asking medical providers for batches of information about members of their units, according to the outlet.

However, commanders can act on information sent from higher headquarters indicating that a soldier’s medical record contains a past diagnostic code associated with gender dysphoria.

The Army order also reportedly directs medical providers to notify commanders when annual physicals identify a current or past diagnosis.

Separations Continue as the Policy Faces Court Challenges

The Pentagon began implementing the current policy after President Donald Trump issued an executive order in January 2025 directing the military to change its standards for transgender service members.

Defense Secretary Pete Hegseth subsequently issued guidance barring people with a current diagnosis or history of gender dysphoria, or symptoms consistent with it, from military service except under limited circumstances.

The Pentagon later offered affected active-duty and reserve troops periods in which they could identify themselves and voluntarily separate before the military moved toward involuntary separations for those who remained.

The policy has faced multiple federal court challenges since shortly after Trump issued the executive order in January 2025.

In May 2025, the Supreme Court allowed the Pentagon to enforce the policy while litigation in Shilling v. United States continued, staying a preliminary injunction issued by a federal judge in Washington state. The Supreme Court did not rule at that stage on whether the policy itself was constitutional.

A separate challenge, Talbott v. United States, remains pending. In June 2026, the U.S. Court of Appeals for the D.C. Circuit upheld a preliminary injunction protecting the current service-member plaintiffs in that case while narrowing the scope of the lower court’s order.

The Trump administration filed a petition with the Supreme Court on Aug. 27 asking the justices to review the D.C. Circuit’s ruling.

The government argues that decisions about medical qualifications for military service warrant significant judicial deference and that the policy does not violate the Fifth Amendment’s equal-protection guarantee.

Attorneys representing the service members argue the policy unlawfully discriminates against transgender troops and excludes people who are otherwise capable of meeting military standards.

The new identification effort is affecting active-duty and reserve personnel, as well as service academy and ROTC cadets, according to Federal News Network.

SPARTA Pride, an advocacy organization for transgender service members, and an attorney representing affected troops told the outlet that several hundred people may have been identified through the process during the past two months.

The Defense Department has not publicly confirmed that figure.