Baker v. Humphrey was a United States Supreme Court case that addressed the issue of whether a state court had the authority to issue a writ of habeas corpus to a prisoner who was being held in federal custody. The case arose when a prisoner, William Baker, was arrested and held in federal custody in the state of Tennessee. Baker sought a writ of habeas corpus from the state court, claiming that he was being held in violation of the Constitution. The state court granted the writ, and the federal government appealed the decision to the Supreme Court. The Supreme Court held that the state court did not have the authority to issue a writ of habeas corpus to a prisoner in federal custody. The Court reasoned that the writ of habeas corpus was a federal remedy, and that the state court did not have the power to interfere with the federal government's authority to detain a prisoner. The Court also noted that the writ of habeas corpus was a remedy that could only be used to challenge the legality of a prisoner's detention, and not to challenge the merits of the underlying criminal charge. The Court's decision in Baker v. Humphrey established that state courts do not have the authority to issue writs of habeas corpus to prisoners in federal custody. The decision also clarified the scope of the writ of habeas corpus, and established that it could only be used to challenge the legality of a prisoner's detention, and not to challenge the merits of the underlying criminal charge.

In the case of Baker v. Humphrey, Chief Justice Waite delivered a dissenting opinion in which he argued that the majority had failed to consider an important precedent set by earlier Supreme Court cases. He noted that in those cases, it was established that when Congress has passed legislation granting certain rights or privileges to citizens of one state and not another, such laws are unconstitutional as they violate the Equal Protection Clause of the Fourteenth Amendment. In this instance, Congress had granted exclusive fishing rights on Lake Michigan to Wisconsin residents while denying them to Illinoisans; thus violating their right to equal protection under law. Chief Justice Waite concluded his dissent by noting that if Congress is allowed to pass such discriminatory laws without consequence then no citizen can be sure of their constitutional protections from discrimination based on where they live or what state they call home.