Since the time of the drafting of the Fifth Amendment, there has been a debate over which constitutional protections are applicable to courts-martial. The text of the amendment exempts only the requirement of a grand jury indictment. Though it was universally understood at the time of the Founding that jury trials did not apply to courts-martial, there is no such textual exception in the Sixth Amendment. An earlier draft presented to Congress did specifically exclude military trials from the jury guarantee, but that version was rejected. Perhaps the Framers believed that the exemption to jury trials was so universally recognized that it would have been redundant to have specified it.

During the Virginia ratifying convention, Anti-Federalists Patrick Henry and George Mason feared that the lack of a bill of rights would permit Congress, as Henry stated, to “inflict the most cruel and ignominious punishments on the militia,” implying that there was a danger of establishing a national standing army. But it does not necessarily follow that the Fifth Amendment was intended to apply to military defendants, although in contemporaneous British practice, the protections against double jeopardy and self-incrimination were accorded to defendants in military trials. Early in the eighteenth century, Sir Matthew Hale declared that members of the military should not be subject to courts-martial during peacetime, a principle Sir William Blackstone confirmed in his Commentaries on the Laws of England (1765–1769). How much of British practice was to be carried over into the legal obligations of the American Constitution is difficult to discern. The Framers and ratifiers are virtually silent on the matter.

It seems clear enough that the Framers intended Congress to have plenary authority to define the rules regulating the armed forces (Article I, Section 8, Clause 14), at least in relation to what the executive is permitted to do, and perhaps to the judiciary as well.

In fact, subsequent to the ratification of the Fifth Amendment, the courts left it to Congress to define offenses against the military and the manner of their being adjudicated. Judicial review of decisions of military tribunals was very limited. In 1950, the Supreme Court, in Johnson v. Eisentrager, held that German nationals in U.S. Army custody in Germany after their conviction by a military commission of violating the laws of war had no right to the writ of habeas corpus to test the legality of their detention. In the course of reaching that conclusion, the majority reasoned that enemy aliens have no greater rights than Americans, and that “American citizens conscripted into the military service are thereby stripped of their Fifth Amendment rights and as members of the military establishment are subject to its discipline, including military trials for offenses against aliens or Americans.” The Court further emphasized that the military has “well-established . . . power . . . to exercise jurisdiction over members of the armed forces. . . .” If the military tribunals acquire “lawful authority to hear, decide and condemn, [then] their action is not subject to judicial review merely because they have made a wrong decision on disputed facts.”

On the other hand, the Uniform Code of Military Justice (1950), supplemented by the Manual for Courts-Martial, affirmatively grants due process rights essentially comparable to those in a civilian court, such as the guarantee of counsel, protection from self-incrimination and double jeopardy, and being advised of rights before interrogation; and the Court of Military Appeals (renamed the United States Court of Appeals for the Armed Forces in 1994) has held that service members are entitled to all constitutional rights except those that are expressly or by implication inapplicable to the military. United States v. Clay (1951); United States v. Jacoby (1960).

The only appeal to an Article III court permitted by the Uniform Code of Military Justice is to the Supreme Court by writ of certiorari from a decision of the United States Court of Appeals for the Armed Forces. Nonetheless, federal courts will review cases collaterally, primarily through the writ of habeas corpus. Until 1953, such collateral review centered on the question of whether the military tribunal possessed proper jurisdiction. Hiatt v. Brown (1950). Review remained highly deferential. For the civilian courts to entertain a petition on a writ of habeas corpus, the petitioner must be in actual military custody, and he must have exhausted all available legal remedies within the military justice system.

In 1953, the Supreme Court opened a new avenue of appeal. In Burns v. Wilson (1953), a decision that remains highly controversial, a plurality of the justices declared that military courts had the same responsibility as civilian courts “to protect a person from a violation of his constitutional rights.” But the justices also stated that the requirements of military discipline may result in an application of constitutional rights different from those accorded to civilian defendants. Finally, the justices stated that civilian courts could review claims de novo, but only if the military courts had “manifestly refused to consider” the petitioners’ assertions of error.

Rasul v. Bush (2004), relying on Burns and other cases, read Eisentrager narrowly and held that the federal habeas statute now confers federal district court jurisdiction to hear challenges of alien detainees held at Guantanamo Bay. However, the Court explicitly did not decide the substance of those rights and limited the habeas extraterritorial reach to Guantanamo Bay, which it said had a unique relationship to the United States. At the same time, in Rumsfeld v. Padilla (2004), the Court, on jurisdictional grounds, avoided ruling on the extent of the president’s power to keep a U.S. citizen in military custody as an enemy combatant; but in Hamdi v. Rumsfeld (2004) the Court decided, without a majority opinion, that the government must give a U.S. citizen held in the United States some type of hearing at which he can contest the facts on which the government decided to treat him as an enemy combatant.

Subsequently, the Court held in Hamdan v. Rumsfeld (2006) that a presidential order that directed the trying of alien combatants by military commission exceeded procedural protections afforded by the Uniform Code of Military Justice and the Geneva Conventions (1949). The Court would allow the executive to create deviations from the required procedures only to the extent that “the exigencies .  .  . necessitate” it. The Court had also held that the Detainee Treatment Act of 2005 did not strip the Court of jurisdiction to hear habeas corpus petitions in cases begun before the Act went into effect.

In response, Congress passed the Military Commissions Act of 2006 applying the restriction of habeas corpus petitions even to ongoing cases. In Boumediene v. Bush (2008), the Court held that the procedures established in the Detainee Treatment Act and the Military Commission Act were “not an adequate and effective substitute for habeas corpus” that was available to aliens held in Guantanamo Bay. Subsequently, by July 2010, nineteen of thirty-four detainees won release from Guantanamo on the grounds of insufficient evidence. However, in Al-Adahi v. Obama (2010) and Latif v. Obama (2011), the D.C. Circuit regularized the methods for evaluating evidence for the lower federal courts, and far fewer detainees succeeded in their habeas corpus petitions.