The Pentagon recently released its plan to better integrate transgender troops into the military, providing guidance to service members already in and a road map moving forward for transgender troops who wish to join.
Department of Defense Instruction 1300.28 says that troops who are mentally a different gender than they are physically will start by visiting a military doctor to receive a diagnosis. If the doctor agrees and diagnoses the service member, then the service member alerts their chain of command and begins a process that is tailored to each individual.

To summarize the process in broad strokes, the doctor and service member will agree on a treatment plan that addresses the member’s mental and physical health, and the member will report it to their commander. This plan will include an estimated day when the member’s gender will be officially switched in the Defense Enrollment Eligibility Reporting System.
This official switch in DEERS won’t typically happen until the doctor has asserted that the transition is complete, the commander has signed off on the change, and the member has produced a court order, passport or state birth certificate asserting their preferred gender.
Once the member’s status is changed in DEERS, he or she will — as far as the military is concerned — cease to be their birth gender and will instead be recognized as their preferred gender. This includes uniform standards, physical training tests and all other regulations that refer to gender.
Also, the guidance stipulates that service members should not begin living as their preferred gender on duty until they complete their transition. This is because they will still be expected to conform to uniform and other regulations that apply to their birth gender until they complete their transition.
The DoD Instruction letter lays out guidance for commanders, including when they should delay a member’s transition or specific steps in the process to protect mission effectiveness. Basically, the commander should use the same discretion they have with other aspects of a member’s medical care and, when necessary, order the soldier to delay treatment in order to accomplish a mission.

These delays could be ordered when the transgender soldier is in a mission critical or shortage job, is deploying, or the transition could cause a breakdown in unit readiness at a key time.
Troops who need cross-sex hormone therapy to complete their transition or maintain their preferred gender will receive it within the constraints of their unit missions.
The instructions also addressed the expectation that transgendered people might soon join the military and attempt their transition early in their enlistment or time as an officer.
The instructions strongly deter this, advising commanders that while there is no blanket prohibition on gender transition in the first term of service, the necessities of training troops and preparing them for their overall military career will often preclude the service member’s ability to complete their transition.
So, people who want to transition to another gender and serve in the military should either transition before their enlistment or serve their first contract before beginning treatment.
The instruction is surely controversial. Secretary of Defense Ash Carter has defended it, but Texas Rep. Mac Thornberry, the chairman of the House Armed Services Committee, has slammed it as dangerous and ill-thought out. He cited recruiting and deployability concerns.