Jefferson ran again against Adams in 1800 with Aaron Burr of New York as his Vice Presidential running mate and the Democratic-Republican ticket elected 73 electors, a majority of the electors.  However, the Electoral College had been designed without political parties in mind: the 73 Democratic-Republican electors all cast one vote for Jefferson and one vote for Burr.  Jefferson and Burr thus tied and as the Constitution provided (Article II, section 1.3) the election went into the House of Representatives with each state delegation casting one vote.

At that time there were sixteen states and a majority -- nine states -- was required for victory.  Many of the Federalist in the House supported Burr, who was viewed as an opportunist, but as less dangerous than the more radical Jefferson.  On the first House ballot, Jefferson received the votes of eight states and Burr six.  Two states -- Maryland and Vermont -- could not vote because neither candidate received the majority support of the state delegation.  With no majority, the House deadlocked for six days with multiple ballots.

Alexander Hamilton, however, had more serious reservations about the integrity of Burr, a fellow New York lawyer, and he supported Jefferson.  Hamilton was incredibly frank in his opposition to Burr and blunt in his language.  He wrote to U.S. Senator James Ross of Pennsylvania, a leading Federalist:

"I can pronounce with confidence that Mr. Burr is the last man in the United States to be supported by the Federalists.

. . .

"First, it is an opinion firmly entertained by his enemies and not disputed by his friends, that, as man, he is deficient in honesty." (Hall, page 229)

Hamilton continued in this vein, listing six more deficiencies.  With Hamilton's ferocious support, Jefferson was elected the third President of the United States by the House of Representatives on February 17, 1801.  Aaron Burr became Vice President.

Jefferson, however, would not take office until March 4, 1801, and the Federalists continued to fear the radical Jefferson and the Democratic-Republicans.  Using their control of the Congress and the Presidency, they had been creating, by law, new judgeships and nominating and approving judges, the "Midnight Judges," to fill the positions.  In their haste, they were not able to deliver the commissions to all of the newly appointed judges before Jefferson assumed office.  On March 4, Jefferson became President and Madison his Secretary of State.

At that time there was no Justice Department: the State Department performed many of the functions that today would be the province of the Justice Department.  One of Madison's first actions (or non-actions) was to refuse to deliver the remaining commission to the would be judges, including one William Marbury.  Marbury sued Madison for his commission.  Madison played a minor role in the development of judicial review.  Madison supported judicial review of state actions: it was essential to the survival of the federal government.  However, from their actions we know that neither Jefferson nor Madison believed that the Supreme Court had the authority to review their actions. Nonetheless, Madison refused to deliver the commission to Marbury; thus his name is forever linked to the Supreme Court case that first asserted judicial review of the actions of another branch of the federal government.

The Democratic-Republican party nominated its candidates by Congressional caucus of party members in both Houses.  With Jefferson's support Madison won the Democratic-Republican nomination for President in 1808.  Aaron Burr, Revolutionary War hero and Jefferson's first Vice President, might have seriously contested Madison for the nomination, but Jefferson had carefully maneuvered the second term Vice Presidential nomination away from him.  Burr ran for Governor of New York, but was defeated in part due to the intervention of Hamilton.

Burr challenged Alexander Hamilton to a duel and killed him in Weehauken, New Jersey, in 1804.  The needless death of a man who had served his country in the Revolution and in the development of the Constitution was viewed as an outrage, and Burr was indicted for murder in both New York and New Jersey.  The indictments eventually were dropped, but Burr involved himself in increasingly fanciful schemes to detach the states and territories west of the Appalachians from the Union.  His career self-destructed, and in 1808 he slipped quietly out of the country.

In the general election, Madison was challenged by two Democratic-Republicans defectors.  Clinton, the party caucus' nominee for Vice President, was simultaneously a candidate for President.  In office, Jefferson and Madison had more toward the center: the more radical Democratic-Republicans were disaffected and nominated James Monroe.  The sole Federalist candidate was Charles Cotesworth Pinckney of South Carolina.

In the end, the Democratic-Republican defections had little impact on the results.  Clinton won only six of New York's nineteen electors and Monroe was trounced in Virginia.  Madison was comfortably elected fourth President.  George Clinton was elected Vice President with him, but was to die in office.

During Madison's first term the charter of the Bank of the United States came up for renewal.  Albert Gallatin, who had been Jefferson's Secretary of the Treasury and was continued in that office by Madison, recommended a renewal.  The Democratic-Republican party, including Madison, had opposed the creation of the bank, which had been proposed by Hamilton, and many were disinclined to support a renewal.  Henry Clay of Kentucky, a great admirer of Madison, nonetheless revived the argument that the federal government lacked a constitutional basis for the creation of a national bank:

"Is it to be imagined that a power so vast would have been left by the wisdom of the Constitution to doubtful inference?"

The renewal of the charter was postponed by the House by a vote of 65-64, in effect a defeat since the charter would expire without action.  It was defeated in the Senate when Vice President Clinton broke a 17 to 17 tie with a vote against renewal.

Gallatin tendered his resignation in March, 1811, but Madison declined to accept it.  Instead Madison took the first step to strengthen his cabinet.  Robert Smith had served eight years as Jefferson's Secretary of the Navy and two years as Madison's Secretary of State, but demonstrated little loyalty to Madison.  Smith and his brother, a radical Democratic-Republican Senator from Maryland, had opposed the renewal of the charter.  Although Madison had done little to aid Gallatin, he forced the resignation of his Secretary of State.

James Monroe had diplomatic experience in London and Paris, and had the support of the radical wing of the party.  Madison sought him for his new Secretary of State.  The relationship of Madison and Monroe had been difficult: Monroe had run for office against Madison twice and had opposed him at Virginia's ratifying convention.  Monroe had lost all three times.  The last defeat, in the Presidential election of 1808, had been humiliating.  Monroe had returned to Virginia and, to restore his credibility, had contested and won the election for Governor.  Nonetheless, he answered Madison's call and was to prove loyal and effective in Madison's cabinet.

In the Northwest Territory, the Shawnee chief Tecumseh was attempting to rally the Nations against the White advance.  He went south to recruit the Southern Nations.  In his absence, his brother, know as the Prophet, attacked a force commanded by William Henry Harrison near Tippecanoe, a small tributary of the Wabash River in Indiana.  The Prophet was not so much defeated as discredited: his assurances of Native American invulnerability were proved wrong in a long, bloody and indecisive battle.  Tecumseh's plans for a grand alliance were shattered.

Madison was re-nominated in 1812 by the Democratic-Republican congressional caucus, but John Langdon of New Hampshire declined the Vice Presidential nomination.  The caucus then gave the nomination to Elbridge Gerry, recently defeated for reelection to the governorship of Massachusetts.  Madison was opposed for the Presidency by DeWitt Clinton of New York who would become more famous for the construction of the Erie Canal.  Madison lost both New York and Massachusetts, two big states.  But he carried Pennsylvania and Virginia and enough states to win in the Electoral College by 128 to 89.  Gerry was elected with him, but, like George Clinton, he died in office.  Gerry is much better known, however, for a venerable weapon of party competition to which his name is attached, the Gerrymander.