Jefferson's inaugural address was a commitment to ongoing change through the democratic process. He named "absolute acquiescence in the decisions of the majority the vital principle of republics, from which there is no appeal but to force." The principle demanded freedom of opinion and debate, including the right of any minority to turn itself into a new majority. "If there be any among us," Jefferson said, "who would wish to dissolve this Union or to change its republican form, let them stand undisturbed as monuments of the safety with which error may be tolerated where reason is left free to combat it." This was the authentic revolution of 1800. Because of it, the Constitution became an instrument of democracy, change became possible without destruction, and government could go forward with the continuing consent of the governed.
The new president named to his cabinet men known to be moderate Republicans. The Federalists' fears were assuaged; Republicans of a more radical persuasion were disappointed. James Madison, the secretary of state, had been Jefferson's political friend and partner for many years. Secretary of War Henry Dearborn and Attorney General Levi Lincoln were Massachusetts Republicans appointed, in part, to nudge that important state into the Republican column. Robert Smith, the secretary of the navy, owed his appointment to his brother, Samuel Smith, the influential representative of Baltimore's mercantile Republican interests. Albert Gallatin of Pennsylvania was the only controversial appointment. His Swiss birth, forensic prowess, and wizardry with treasury figures had combined to make the forty-year-old congressman a Federalist whipping boy. But Jefferson prized Gallatin's abilities, and the new secretary, who had been a sharp critic of Hamilton's fiscal policies, proved to be a force for moderation in the administration. The stability and harmony of this cabinet would never be equaled. In the eight years of Jefferson's presidency, only the part-time office of attorney general changed hands.
The model of executive unity, concentrating all powers of decision in the president, had been established by Washington, then had broken down under Adams. Jefferson restored it, but he dominated his administration more surely and completely than Washington had done. To the formal authority of the office, Jefferson added the authority of party leader. He had enormous public prestige as the spokesman of republican principles and national ideals. By some personal magnetism he drew men to him, persuaded them to follow, and inspired their loyalty. His style of leadership was averse to dissension and controversy. He sought to engender amiability and, wherever possible, to grasp "the smooth handle." Business was conducted through day-to-day consultation with the secretaries. The cabinet met infrequently, but when it did, usually on critical foreign problems, Jefferson invariably managed to produce a consensus. He led without having to command; he dominated without ruling.
Jefferson also dominated Congress. In 1801, for the first time, the Republicans controlled both houses of Congress. The Federalists were a shrinking minority, yet they were by no means powerless. Their obstructionist tactics would have proved very damaging if the Republicans had not stuck together. In Republican theory, borrowed from the Whig theory of the Revolution, Congress was superior to the executive and the executive should not interfere in legislative business. Jefferson honored the theory, at least in official discourse, but he recognized that practically the government demanded presidential leadership if any majority, whether Federalist or Republican, was to carry out its program. Congress could not lead. During the Federalist decade it had performed best under Hamilton's ministerial guidance. The problem had been easier for the Federalists, for they had no "least government" dogmas to overcome, no deep-seated fears of "monarchical" power; and compared to the Republicans, they formed a fairly cohesive body. The Republican majority was a loose coalition of jarring interests, experienced only in opposition and jealous of executive power.
How, then, could the Republican president overcome the "separation of powers" and make Congress an effective instrument for realizing the administration's objectives? The solution was found partly in the personal influence Jefferson commanded and partly in the network of party leadership outside constitutional channels. As the unchallenged head of the Republican party, Jefferson acted with an authority he did not possess—indeed, utterly disclaimed—in his official capacity. His long arm reached out, usually through cabinet officers, to Capitol Hill, where the leaders of both houses were his political lieutenants. Presidential leadership was thus locked into congressional leadership. And despite the weak structural organization of the Republican party in Congress, it was a pervasive functional reality. The president chose a newspaper, the National Intelligencer, in the capital as the administration organ; he kept up a steady stream of communication with Congress and party leaders; he turned his house into a kind of social club and spent countless weary hours and a substantial part of his $25,000 salary entertaining congressmen. (A widower, he had no "first lady", Dolley Madison sometimes performed that role, as did Jefferson's elder daughter, Martha, on her visits to the capital.)
The president was not only chief magistrate but chief legislator as well. Nearly all the legislation during eight years originated with the president and his secretaries. Lacking staff support of any kind, Congress depended on executive initiatives and usually followed them. Federalist congressmen complained of the "behind the curtain" or "backstairs" influence of the president. Eventually some Republicans rebelled. But the system of presidential leadership worked with unerring precision during Jefferson's first term. It worked less well once the Republicans, with virtually no opposition to contend against, began to quarrel among themselves, as they did during Jefferson's second term; and it would not work at all under his successor, Madison, who lacked both his public authority and personal magnetism.
During the early months, Jefferson found the task of making appointments to office exceedingly irksome. Not counting military officers, postmasters, and other minor civil functionaries, there were 316 major offices in the gift of the federal executive. They were monopolized by Federalists. Jefferson's preference was to remove as few as possible, with a view to converting the mass of Federalists to the Republican cause. He was repelled by the principle, already reduced to practice in New York and Pennsylvania, of making party affiliation the sole or primary test of public appointment. The politics of spoils and proscription degraded republican government. Nothing more should be asked of civil servants, he said, than that they be honest, able, and loyal to the Constitution. As important as the principle was in the abstract, it was more important in practice because of its obvious fitness to the attainment of the political harmony and consolidation envisioned in the inaugural address.
Many Republicans, whether from partisan principle or interest, disagreed with this strategy. The Federalist leaders, some said, were incorrigible; any temporizing with them would only disgust the mass of Republicans and jeopardize the administration. Others hungered for the spoils of victory. If the expulsion of Federalists and the appointment of Republicans "should not be the case, for what, in the name of God, have we been contending?" they asked. At the outset, Jefferson held his ground. He limited removals to two classes of officeholders. The first was Adams' "midnight appointments"—indeed, all appointments except judgeships in good behavior made after 12 December 1800, when the president knew he had been defeated. This office-packing by a lame-duck administration was intolerable, and Jefferson considered all these appointments "nullities." The second class included officials found guilty of misconduct. Jefferson especially had in mind federal marshals and attorneys who had forfeited the public trust by their enforcement of the Sedition Act. By January 1802 he counted twenty-one removals of midnight appointments and fifteen removals for misconduct of any kind.
Within a few months partisan pressures from both sides caused the president to modify his patronage policy. The issue came to a head in Connecticut, where the Federalists controlled everything; the Republicans were weak, systematically excluded from the state government, and treated as outcasts of society. Only by federal appointment could they get a political foot in the door. When Jefferson removed a midnight appointment and named a Republican in his place as collector of the port of New Haven, the local merchants and Federalists angrily remonstrated. In reply, Jefferson defended his actions and the right of the Republicans to a fair share of the federal offices. Continued Federalist monopoly defeated the will of the people. "If a due participation of office is a matter of right, how are vacancies to be obtained?" he asked. "Those by death are few; by resignation, none. Can any other mode than that of removal be proposed?" Heretofore the answer had been yes, the mode of conciliation and conversion; and the idea that party allegiance alone was just ground for removal or that the subordinate offices should rotate with the popular will had been rejected. Proposing now, in the summer of 1801, before this demonstration of Federalist intransigence to give the Republicans "a proportionate share" of the offices, Jefferson introduced the partisan standard of removal and appointment in the federal government. In practice, he showed a good deal of flexibility, adapting the policy to varying local situations. By the end of 1803, he had appointed Republicans to one-half the major offices. Federalist patronage, like the party, had been elitist. Jefferson broadened the base of the civil establishment, taking in more westerners and more men of talent without wealth, privilege, or status, thereby making it more representative of American society.
The Republican ascendancy embittered the shrinking Federalist minority. Thomas Paine's return to the United States at the president's invitation in 1802 started up the old slanders of Jacobinism and infidelity. At the same time Jefferson faced a new libel by the grubstreet journalist and disappointed office-seeker James T. Callender, adopted by some of the Federalists, that he had for many years kept an "African concubine," Sally Hemings, at Monticello and was the father by her of several slave children. Thus began the prolific career of a story that would on occasion figure prominently in accounts of Jefferson's personal life, which were necessarily speculative because of his care in guarding his privacy. As with other libels about him, he never replied publicly to this one, doubtless on the theory that any reply would only stimulate rather than arrest it. Moreover, he was committed to what he called his "experiment" in unfettered freedom of the press; and although he twice acquiesced in state prosecutions for libel, he did no injury to that experiment. Almost two centuries later, in the fall of 1998, the results of DNA testing of Jefferson and Hemings descendents provided support for the idea that Jefferson was the father of at least one of Sally Hemings' children, Eston. But in the absence of direct documentary evidence either proving or refuting the allegation, nothing conclusive can be said about Jefferson's relations with Sally Hemings.