Pentagon searching medical records to identify transgender troops

The military is searching protected medical records to find transgender troops who have tried to continue serving amid the Trump administration’s ban on trans Americans in uniform, multiple sources tell Federal News Network.

Commanders around the world have started receiving notices that members of their units are violating Pentagon policy, and are being instructed to begin the separation process. The sweep is believed to have outed several hundred active-duty and reserve troops, including service academy and Reserve Officer Training Corps cadets, over the past two months, according to the trans advocacy nonprofit SPARTA Pride and Priya Rashid, an attorney with the National Institute of Military Justice.

The Pentagon is moving to separate troops as multiple lawsuits challenging the ban move through the federal court system. In August, the administration petitioned the Supreme Court to weigh in on whether the policy is unconstitutional before a key case goes to trial in January.

The situation has spurred a military-wide scramble to cover the work of troops placed on leave, connect them with legal help and, in some cases, find money and lodging for those facing homelessness.

“The military was my life; it was my everything. I gave my entire self to my job and to my country, and I was serious about my career,” one sailor said. “They’re about to completely upend my life and my career, and I’m not prepared for that.”

Finding trans troops

The Trump administration argues that any history of gender dysphoria, the medical condition where a person’s gender identity doesn’t match their biological sex, is incompatible with “high standards for troop readiness, lethality, cohesion, honesty, humility, uniformity and integrity.” 

After President Donald Trump returned to office in January 2025, the Pentagon issued directives that formed the basis of the ban. It initially allowed troops to leave during a grace period that ended in July 2025, then began removing them itself. 

Now SPARTA officials say dozens of people have reached out to report “unprecedented use of military medical systems to identify individuals.”

Five sources, including two transgender service members facing separation after their gender dysphoria-related diagnoses were flagged to their commands, described what they called a “witch hunt” for honorably serving troops. Three were granted anonymity because they fear retaliation. 

Documents obtained by Federal News Network indicate that, in some cases, the information is coming from the Pentagon’s highest echelon.

The Office of the Secretary of Defense has identified service members “who may have a current diagnosis or history of or exhibit symptoms consistent with gender dysphoria in their electronic healthcare record,” according to an internal Air Force email sent July 31 and viewed by Federal News Network. 

Spokespeople for the Defense Department, the Defense Health Agency and each of the military services declined to answer emailed questions, citing ongoing litigation.

Sources believe the military is digging through MHS Genesis, DoD’s electronic health records system, and other databases to find remaining transgender troops. The system contains medical histories, prescriptions, mental health notes, TRICARE-covered civilian care documentation and even records from before members joined the military. Personnel databases can also reveal changes in a person’s listed gender over time. 

Some, but not all, transgender people experience gender dysphoria; it can be resolved through treatment. Kara Corcoran, SPARTA’s executive director, who is an active-duty Army infantry officer facing separation, said people are being punished for successfully addressing a past medical issue.

“A new line has just shifted and said that these people are inadequate for being able to serve,” she said.

Those details are being shared with unit leaders across the force in conversations and memos from local medical and legal offices, alarming some who argue it violates troops’ privacy and doctor-patient confidentiality.

One separation referral sent to an airman’s commander quoted directly from the service member’s health history, including when they sought treatment for gender dysphoria, their number of counseling sessions and prescribed medication. 

The airman said they were never evaluated in order to receive the separation referral, do not currently experience dysphoria and had not shared details of their past treatment with their colleagues.

A widening sweep

SPARTA estimates thousands of trans troops have been kicked out or are in the process of separating, including those placed on leave until their discharge. 

Still, it’s difficult to pinpoint the number of service members who identify as transgender. DoD estimated around 4,200 troops with gender dysphoria were in uniform when the ban began. That’s about four times higher than in 2019, when the department told a congressional defense committee that about 1,000 currently serving troops were diagnosed with at least one of seven medical codes related to the condition — a figure pulled from Military Health System data. Other outside estimates have ranged from about 6,000 to as many as 25,000 people.

Out trans members who publicly transitioned were among the first to go when the policy changes began. But that’s no longer the case in the ban’s second year, sources said.

Rashid, who represents many of the trans troops in their separation cases, said her calls have exploded over the past two months, with about 25 people reaching out each week for advice on involuntary separation procedures. 

She said she’s heard from many troops younger than 21 who transitioned before joining the military and served in accordance with regulations for their preferred gender from the start.

The latest phase is also flagging older people who transitioned years ago, when they could do so without penalties, and whose current colleagues may not know. The Pentagon is identifying people whose medical notes reference a current or previous transition but who haven’t changed their names or gender markers, as well as those who continue to meet the appearance and fitness requirements of their biological sex.

They are also identifying troops diagnosed with gender dysphoria who didn’t transition, those who sought treatment outside the military but used TRICARE, and those who detransitioned to save their jobs.

“They didn’t do anything wrong,” Rashid said. “They followed the rules and policies and procedures of the year that they were in. We were the ones who changed the rules on them.”

The search is also catching people who aren’t transgender, she said, including members who underwent procedures such as mastectomies or hysterectomies or sought a gender dysphoria diagnosis to obtain treatment for other conditions. 

The cost of separation

The airman and sailor who spoke to Federal News Network after their commands were told to remove them are grappling with the policy’s repercussions for their lives and for the units and country they serve.

Neither opted for a voluntary separation, a term many dislike because it implies they want to cut their military career short.

“I gave my word and swore an oath to my country … to serve my country honorably and to be an asset to the Navy’s warfighting capabilities,” the sailor said. “To voluntarily step away from that felt like a betrayal and a slap in the face to the Navy.”

While the Air Force appears to be processing cases through the medical establishment, the sailor said their local legal staff told them they meet the requirements for administrative separation. They believe their psychiatric records were searched for notes from clinical visits where they confidentially discussed a desire to transition.

Leaving the military would rob their unit of critical combat systems expertise others don’t have, they said. Shipmates who are underway have continued to call for technical support, forcing the sailor to “basically act as customer service over the phone to a ship in the middle of the ocean.”

“For both transgender service members and people who have served with them, we’re all absolutely f***ing livid,” the sailor said. “We have an absolute manning crisis… The more sailors you take off of these ships, transgender or not, you are directly contributing to them not being able to meet mission requirements.”

The airman knows they could earn more in the private sector but worries their departure could hurt the unit’s readiness and cohesion. They’re relieved they might soon be able to openly live as transgender, while grieving the loss of a life and career they love.

“‘My God, it’s finally over, and it wasn’t because I quit,’” the airman recalled thinking when they were told of their pending discharge. “I never gave up.”

What the military can see

MHS Genesis hosts the patient data of more than 9.5 million troops, spouses and children. Authorized users can search military health databases by diagnosis code to identify people with a certain condition and create registries of patients with particular ailments. 

For instance, Military Health System software has been used to track outbreaks of communicable diseases, and identify people at high risk for bone marrow abnormalities.

MHS records have also been used to research service members with gender dysphoria-related diagnoses before. The 2019 report to the House Armed Services Committee lists the specific codes used to identify troops in the MHS Data Repository, including five that fall under gender dysphoria, one for cross-dressing fetishes and one for a history of sex reassignment. 

Military medical providers have also relied on that data for studies on issues like inequities in hormone prescriptions for active-duty troops with a gender dysphoria-related diagnosis.

Health privacy laws are more complicated inside the U.S. military. To ensure enough troops are fit for duty at any given moment, HIPAA allows military treatment facilities to disclose protected health information to a service member’s command.

But the Military Health System says that information remains protected under the Privacy Act of 1974, which generally bars disclosure without written consent except in certain circumstances. Those exceptions include cases where an agency’s employees “have a need for the record in the performance of their duties,” according to statute.

The administration appears to be relying on a provision of the 2023 National Defense Authorization Act designed to reduce the stigma around mental health treatment, Rashid said. Congress directed the Defense Department to protect the confidentiality of mental health services except in exigent circumstances. That can allow disclosure when national security, safety or good order and discipline are at stake.

Rashid argues those exceptions don’t apply to transgender troops being removed from the military, including F-35 avionics technicians, pilots, air defenders and surgeons.

“These are zero-fail tasks that would require a high level of occupational finesse, a high level of technical proficiency,” she said. “Mentally unwell people would have a very difficult time.”

The separation process

The Pentagon’s initial guidance on identifying trans troops explicitly said it would do so using medical records. That’s evolved over time.

A March 2025 DoD memo noted that reviewing medical records would be the “primary means” of identifying troops with a history of gender dysphoria. Two months later, another memo clarified that the services should look to troops’ annual checkups and bloodwork to find instances of dysphoria.

“The secretaries of the military departments will direct unit commanders — working in coordination with supporting medical assets — to ensure service members comply with their [Individual Medical Readiness] program obligations and will immediately commence the identification of affected service members,” the May 2025 memo said.

“Commanders who are aware of service members in their units with gender dysphoria, a history of gender dysphoria, or symptoms consistent with gender dysphoria will direct individualized medical record reviews of such service members to confirm compliance with medical standards under the IMR program,” it added.

That process looks slightly different in each branch of the armed forces. An internal Army order, which was issued in August but was not made public, formalizes a monthslong blueprint for ousting soldiers.

The order, obtained by Federal News Network, explicitly bars commanders from broadly searching health and personnel records to find soldiers with gender dysphoria, or from asking providers for a batch of information about the people in their unit.

It also stops leaders from ordering a behavioral health consult to confirm whether a person has gender dysphoria unless they have personal knowledge of the diagnosis. That could stem from past conversations with the soldier, their request to follow different grooming standards, social media posts, or “reports from higher headquarters to commanders indicating an individual’s medical records reflect a past diagnostic code consistent with gender dysphoria.” 

The Army noted that the form used at annual physicals now includes questions about gender dysphoria, and tells medical providers to immediately notify commanders of members with current or past gender dysphoria. And it tells commanders to update personnel records to reflect the biological sex of all soldiers, not only those pending separation.

Once a commander has verified that a soldier meets the criteria for separation, they must consult with their legal office and speak with the soldier to start the process.

Units have 30 days to process a soldier for separation after their gender dysphoria diagnosis or symptoms are verified, the memo says. If the soldier opts into a separation board, the hearing must take place no later than 60 days after the board receives the medical confirmation.

“Anyone who gets notified should be talking to Trial Defense Service that week — not after they’ve had time to sit with it,” Corcoran said.

The board’s decision heads to the Army secretary or another authority tapped to approve separations. The service has 90 days to kick out a soldier after authorizing their separation.

Commands across the Army must report their progress to service headquarters twice a month, including separation board dates.

In the Air Force and Space Force, medical readiness boards will determine whether airmen qualify for separation before sending cases to unit commanders, according to the internal email. Commanders then have three business days to send paperwork to a centralized legal team in Washington.

The Navy and Marine Corps have similar processes, with Navy Installations Command handling involuntary separations. Sailors have 10 days to request a separation board or waive that right.

The boards are directed to decide only whether someone was diagnosed with or has symptoms of gender dysphoria, regardless of their character or their job performance. Each service secretary makes the final call on whether to remove them.

At first, the airman debated whether they wanted to face a separation board, calling them “foregone conclusions.” But they want their service to make a difference.

“If my fight can help pave the way for others to freely serve in the future, then it’s absolutely worth it,” they said.

What happens next

Separation measures have continued as trans troops await a federal district court’s decision on who will be covered by a class-action lawsuit. 

Lawyers representing more than two dozen service members warned last month that the Pentagon is expediting removals while a key lawsuit is tied up in appeals. In June, a federal judge allowed Talbott v. USA to become a class action but has not yet said who qualifies to join. The judge’s March 2025 order pausing separations has not taken effect amid administration pushback. 

“The government is moving forward with involuntary separations of plaintiffs in this case,” plaintiff attorneys told the U.S. Court of Appeals for the D.C. Circuit Aug. 17. “For example, the government postponed Lieutenant Junior Grade Clara Winchell’s board of inquiry following the issuance of this court’s opinion, but is now attempting to reschedule it to be held on or before Sept. 15, 2026.”

The Trump administration last month petitioned the Supreme Court to overrule the lower court and let it proceed with separations.

“The authority of the U.S. military to determine who may serve in the nation’s armed forces is a matter of exceptional importance,” the Justice Department wrote. “The court should thus take this opportunity to address the constitutionality of the Hegseth policy and reverse the decision.”

Corcoran said junior enlisted troops are among the most at risk. Those who have served less than six years are ineligible for separation pay, may have to repay part of their enlistment bonus, are last in line for veterans benefits and could become homeless. 

SPARTA has provided more than $36,000 in financial support to 29 recipients so far this year, including four who used the money to leave states with anti-trans laws. 

The airman and the sailor who spoke to Federal News Network both said they’d like to rejoin the military if separated. Current policy bars them from doing so.

“We’ll have our ups, we’ll have our downs, but at the end of the day, I’m still a United States Navy sailor, and I’m more than happy to wear my country’s flag on my shoulder,” the sailor said.

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