In its plan for the federal judiciary, the Congress in 1789 divided the nation into thirteen judicial districts that served as the basic organizational units of the federal courts. In each district, a U.S. district court served as the federal trial court for admiralty and maritime cases as well as for some minor civil and criminal cases. Congress authorized the district judge to appoint a clerk in each district to assist in the administration of the district and circuit courts, and authorized the president to appoint in each district a marshal and federal prosecutor, then called a "district attorney."

The court's jurisdiction was limited to cases arising within the district, and the judges were required to reside in their districts. The original districts outlined by Congress coincided with the borders of the eleven states that had ratified the Constitution, with separate districts for Maine and Kentucky, which were still a part of Massachusetts and Virginia, respectively.

In the early years of the federal government, caseload in the district courts depended largely on the volume of admiralty suits in the region, and some courts heard few cases. District judges also served on the U.S. circuit court that met in their judicial district, and for much of the nineteenth century, district judges were likely to devote more time to their duties on the U.S. circuit courts than to the business of the U.S. district courts. Gradually over the nineteenth century, Congress expanded the jurisdiction of the district courts, especially in the area of non-capital criminal cases.

In the original districts of Maine and Kentucky and in many new states during the nineteenth century, the U.S. district court also exercised the jurisdiction of the U.S. circuit courts until such time that the district was incorporated into a judicial circuit. Appeals from such courts generally went to the Supreme Court and occasionally to the circuit court in another district within the state. Only in 1889 did Congress finally provide a circuit court for every judicial district in the nation and thus end this expanded jurisdiction of certain district courts. In the Judicial Code of 1911, Congress abolished the U.S. circuit courts and made the U.S. district courts the sole general-jurisdiction trial courts of the federal judiciary. Until 1891, when Congress first provided a uniform salary for district judges, compensation varied from district to district according to Congress's estimation of the amount of business expected to come before the court.

As new states entered the union, Congress created additional district courts that in their geographical outline remained within state boundaries, with two negligible exceptions. As early as the 1790s Congress divided some states into multiple districts, each with court staff and separate records of proceedings. Frequently, a single judge served more than one district within a state. The U.S. District Court for New York in 1812 became the first in the nation with two judgeships, but in 1814 Congress divided the state into two judicial districts, each with a single judge. Congress did not create another permanent second judgeship for a district court until 1903 when it authorized an additional judgeship for the Southern District of New York.