The term habeas corpus refers most commonly to the writ of habeas corpus ad subjiciendum, which directs the custodian of a prisoner to bring that prisoner before a court and explain the reasons for his or her confinement. A writ of habeas corpus is a challenge to the legality of a prisoner's detention and does not directly or necessarily entail an inquiry into the prisoner's guilt or innocence. After examining the reasons for confinement, the court that issued the writ may release the prisoner or remand the prisoner into custody. The "great writ of liberty," as it is often called, is a judicial remedy aimed at preventing the arbitrary use of executive power to imprison individuals without just cause.

The use of habeas corpus has roots in English common law dating to the fourteenth century and was made a part of England's statutory law in 1679. American colonial courts issued the writ at common law, and state governments continued to recognize habeas rights following independence. The U.S. Constitution made no explicit provision for the writ, providing only that "The Privilege of the Writ of Habeas Corpus shall not be suspended, unless when in Cases of Rebellion or Invasion the public Safety may require it." In the Judiciary Act of 1789, Congress granted the federal courts authority to issue habeas corpus to prisoners in federal custody or committed for trial before a federal court. In 1807, the Supreme Court noted that federal courts could not issue habeas corpus to prisoners held by state or local governments because Congress had not provided such authority. The Court also held, in 1822 and again in 1830, that federal courts, lacking appellate jurisdiction over criminal cases, could issue the writ only before a prisoner's conviction.

Prior to the Civil War, Congress extended federal habeas rights to state prisoners in two limited ways. In the Force Bill of 1833, Congress authorized federal courts to grant the writ to those in state custody as a result of acts performed pursuant to federal law. The 1833 act was a response to South Carolina's nullification of the federal tariff and the resulting possibility that state officials would jail federal revenue officers attempting to enforce the tariff law. Congress acted again in 1842 to grant federal habeas rights to foreigners held by state authorities for actions performed under the authority of their governments. This extension of the writ was a response to New York's prosecution of a British national for an attack on an American ship, which the federal government desired to treat as a diplomatic, rather than a criminal, matter.

Although a quick resolution of the tariff crisis ensured that the 1833 act was never used in its intended context, the act provided the authority for federal courts to grant habeas to federal marshals held as state prisoners after apprehending alleged fugitive slaves under the Fugitive Slave Act of 1850. In 1859, the Supreme Court held that a state court lacked the power to issue habeas corpus to a federal prisoner convicted of violating the Fugitive Slave Act. In 1871, the Court held that state courts were not permitted to free federal prisoners under any circumstances.

Traditionally, courts accepted the return of the writ at face value and released the prisoner only if the return failed to state an adequate legal basis for confinement. The federal courts during the Civil War began to consider additional evidence in response to petitions from individuals who sought habeas corpus to escape military service on the ground that their alleged enlistment was invalid. Widespread fraud by military recruiters hoping to earn bounties made some federal courts skeptical of the military's claims that the person in custody had in fact enlisted.

Abraham Lincoln's suspensions of habeas corpus during the Civil War-first limited to arrests in certain areas along military transport lines and later expanded to encompass all arrests for disloyal conduct in Union territory-created a conflict between executive and judicial power. Chief Justice Roger Taney, sitting in 1861 on a U.S. circuit court in Maryland, proclaimed in Ex parte Merryman that the suspension power belonged exclusively to Congress and could not lawfully be exercised by the president, although Taney acknowledged that he had no means of compelling Lincoln to obey his decision. Other federal judges receiving petitions for writs of habeas corpus during the war cited Merryman but, like Taney, recognized that practical considerations prevented them from issuing the writ or attempting to enforce a writ military authorities had ignored. In 1863, Congress passed the Habeas Corpus Act, which permitted the president to suspend the writ for the duration of the war but also required the military to report all arrests to the federal courts and to release prisoners not indicted promptly.

Reconstruction led to the most dramatic expansion of habeas corpus in the nation's history, as Congress in 1867, in an effort to protect freedpeople and Union supporters in the South, made the writ available to any person "restrained of his or her liberty in violation of the constitution, or of any treaty or law of the United States," thereby extending the writ to state prisoners claiming that their detention violated a federal right. Habeas corpus for the first time became a post-conviction remedy, as federal courts read the 1867 act as giving them the power to free individuals who had been tried and convicted by state tribunals, and the Supreme Court affirmed this authority in 1886. The 1867 law also authorized a direct appeal from a U.S. circuit court to the Supreme Court, a right extended previously only to foreign nationals seeking habeas corpus under the 1842 statute.

In 1868, the Supreme Court heard the case of Ex parte McCardle , an appeal under the 1867 act by a Mississippi newspaper editor detained by military authorities for publishing anti-government editorials. After the case was argued but before the Court issued a decision, the Republican majority in Congress repealed the Court's appellate jurisdiction over cases brought under the 1867 act (15 Stat. 44), which included McCardle , for fear that the Court would declare Reconstruction laws unconstitutional. Shortly thereafter, however, the Court held in Ex parte Yerger that in cases arising under the act of 1789, it retained appellate jurisdiction, which it could exercise by issuing simultaneous writs of habeas corpus and certiorari. In 1885, Congress restored the right of appeal previously established in the act of 1867.

After Reconstruction, the Supreme Court showed more deference to state criminal proceedings, interpreting its appellate jurisdiction narrowly. Between 1879 and 1915, the Court issued decisions limiting habeas corpus for state prisoners to cases in which the state court lacked jurisdiction, mandating that a state prisoner exhaust all possible remedies in the state courts before seeking habeas corpus from a federal court, disallowing the reexamination of constitutional questions decided by a state court of competent jurisdiction, and holding that habeas corpus would not be granted to a state prisoner if the state had in place an adequate corrective process for the denial of constitutional rights. Congress in 1908 restricted appeals to the Supreme Court under the 1867 act by requiring that the federal judge issuing the decision or a Supreme Court justice certify that probable cause for an appeal existed.

In the late nineteenth century, Chinese exclusion cases became an important source of habeas corpus litigation, particularly in northern California. Between 1882 and 1890, Ogden Hoffman, the area's U.S. district court judge, heard over 7,000 habeas cases involving Chinese individuals detained by immigration authorities upon attempting to enter the United States. The courts were caught between federal statutes that limited the immigration of Chinese laborers and a treaty that protected the rights of Chinese immigrants in the United States to reenter. After thousands of habeas petitions were granted, the Supreme Court issued several decisions limiting Chinese immigrants' access to the courts, culminating in a 1905 opinion providing that the decisions of immigration officials were final and generally not appealable in court.

Extensions of the writ after 1940 focused on providing due process for criminal defendants, and the Supreme Court authorized federal courts to consider issues already examined at the state level. Most significant were a 1942 decision abolishing the rule that habeas corpus could issue only when the confining court lacked jurisdiction and a 1953 decision permitting federal courts to reexamine constitutional issues previously tried and reviewed fully by state courts. As a result, the federal courts exercised an expanded supervisory role over state judicial systems and decided state defendants' federal constitutional rights.

Despite several expansions of habeas rights, Congress imposed some restrictions, including the elimination in 1925 of direct appeals to the Supreme Court, the codification in 1948 of the rule requiring exhaustion of state remedies, and a 1966 provision that factual findings made by state courts would normally be presumed correct, putting the burden on the petitioner to disprove them. In the 1970s and beyond, the Supreme Court also retreated from earlier expansive notions of due process for criminal defendants. In 1976, the Court denied habeas corpus as a remedy for a Fourth Amendment violation when a state court had provided an opportunity for a full and fair litigation of the claim. Decisions in 1977 and 1991 limited, and then overturned, a 1963 opinion waiving the exhaustion requirement when the remedies in question were no longer available at the time of the habeas petition. Congress imposed further limits with the Antiterrorism and Effective Death Penalty Act of 1996, including a one-year deadline to file a petition following a final judgment and a provision that habeas corpus would not be granted with respect to a claim litigated on the merits unless the state court decision clearly contradicted Supreme Court precedent regarding federal law.

The efforts of the United States to combat terrorism after September 11, 2001, led to legislative action regarding the habeas corpus rights of aliens designated by military authorities as enemy combatants. The Detainee Treatment Act of 2005 and the Military Commissions Act of 2006 eliminated such rights for enemy combatants detained at Guantanamo Bay, Cuba, and elsewhere. The Supreme Court overturned these laws in part, however, ruling in 2008 that Guantanamo detainees possessed habeas rights because the United States exercised some sovereignty over that territory - a decision that remained in force as of 2013.