The composition of the judicial branch of the national government was a major point of contention in the early years of Thomas Jefferson's presidency. In 1800, when Jefferson was elected, not a single Republican held a federal judgeship. Republicans were further infuriated by the Federalists' Judiciary Act of 1801, passed on February 27, just five days before Jefferson's inauguration. While the main thrust of the act was the creation of sixteen new federal judgeships to ease the load on the Supreme Court, the most concerning clause, to Republicans, was that which cut the number of Supreme Court Justices from six to five. This would deny Jefferson his first opportunity to appoint a Supreme Court justice, and ensure a Federalist court for years to come. While many radical Republicans insisted that judges should be elected and not appointed, Jefferson was not radical enough to agree, and he did not challenge the powers of the courts. He did, however, challenge Federalist control of the courts.
One of the Jefferson administration's most controversial episodes with the judicial system was the case of William Marbury. On his last day in office, March 3, 1801, John Adams had appointed Marbury, an obscure Federalist, as justice of the peace in the District of Columbia. This was one of many so- called midnight appointments. However, he failed to deliver the commission by midnight of March 3. Jefferson's secretary of state, James Madison, refused to deliver the commission, electing instead to hold the position open for a Republican appointment. Marbury, in response, asked the Supreme Court for a writ of mandamus, which would force Madison to deliver the commission.
The Supreme Court did not rule on the case of Marbury v. Madison until February 1803, before which, Jefferson had successfully won the repeal of the Judiciary Act of 1801. Many Federalists thought their power in the Judiciary had been crushed. However, Chief Justice John Marshall demonstrated the considerable power still wielded by the Federalist-dominated judicial branch in his decision in Marbury v. Madison. Marshall and the court denied Marbury's request for a writ of mandamus, ruling not that he did not deserve it, but rather, that Congress had overstepped its constitutional bounds by giving the Supreme Court the authority to issue such a writ in the Judiciary Act of 1789. This was the first time an act passed by Congress was declared unconstitutional by the Supreme Court. This power, called judicial review, was not invoked again for 54 years, but the precedent had been set.
Meanwhile, Republicans had taken steps to impeach two Federalist judges, John Pickering and Samuel Chase. Pickering was a well-known alcoholic whose actions in the courtroom demonstrated that he was clinically insane. Chase had been one of the most overzealous enforcers of the Alien and Sedition Acts, imprisoning several Republican leaders and journalists. The Senate voted to convict Pickering on March 12, 1804. Chase, on the other hand, was acquitted shortly after. With this acquittal, Jefferson's battle with the judiciary effectively ended. Jefferson did not interfere with the judiciary after 1804, and his relations with the judicial branch as a whole were generally amiable.
Recalling the enthusiasm with which the federal judiciary had enforced the Alien and Sedition Acts, and bemoaning the absence of Republicans in federal judicial positions, Jefferson feared the judiciary would remain a Federalist stronghold and provide a major roadblock to his initiatives. He was further disheartened by John Adams' actions during his final months in office. Between December 12, 1800, when it became clear that he would not win reelection, and the day of Jefferson's inauguration, March 4, 1801, Adams appointed a significant number of federal judges. These midnight appointments consisted exclusively of Federalists, most of which had previous political or familial ties to prominent party members. The nation had never experienced a transition from one party to another in the executive branch, and therefore there was no precedent for how to deal with appointments made by a predecessor of a different party. Jefferson at first declared that he would not dismiss any Federalist appointees. However, under pressure from position-seekers in his party, he later altered that promise, agreeing to dismiss all appointees commissioned by Adams after December 12.
Marshall's decision in Marbury v. Madison has been hailed as one of the most important in US history. The principle of judicial review, not exercised again until 1857, nevertheless has been a major feature of the judicial branch throughout American history. Despite the objections of some of his more radical Republican colleagues, Jefferson did support the principle of judicial review. He simply argued that other branches of the government should have the right to review the constitutionality of laws as well. Since Marshall's opinion contained no claim that the courts alone could declare a measure unconstitutional, Jefferson had no argument with the decision. However, Marshall used a portion of his decision to lecture Madison (and thus indirectly Jefferson, his superior) on his moral duty to deliver the commission, as opposed to his legal obligation. This struck Jefferson as a clear example of Federalist partisanship, and steeled him further in his battle against the courts.