In early February 1861, the states of the lower South established a new government, the Confederate States of America, in Montgomery, Alabama, and drafted a constitution. Although modeled on the U.S. Constitution, this document specifically referred to slavery, state sovereignty, and God. It explicitly guaranteed slavery in the states and territories, but prohibited the international slave trade. It also limited the President to a single six-year term, gave the President a line-item veto, required a two-thirds vote of Congress to admit new states, and prohibited protective tariffs and government funding of internal improvements.

As President, the Confederates selected former U.S. Senator and Secretary of War Jefferson Davis (1808-1889). The Alabama secessionist William L. Yancey (1814-1863) introduced Davis as Confederate President by declaring: "The man and the hour have met. Prosperity, honor, and victory await his administration."

At first glance, Davis seemed much more qualified to be President than Lincoln. Unlike the new Republican President, who had no formal education, Davis was a West Point graduate. And while Lincoln had only two weeks of military experience, as a militia captain, without combat experience in the Black Hawk War, Davis had served as a regimental commander during the Mexican War. In office, however, Davis's rigid, humorless personality; his poor health; his inability to delegate authority; and, above all, his failure to inspire confidence in his people would make him a far less effective chief executive than Lincoln. During the war, a southern critic described Davis as "false and hypocritical...miserable, stupid, one-eyed, dyspeptic, arrogant...cold, haughty, peevish, narrow-minded, pig-headed, [and] malignant."

Following secession, the Confederate states attempted to seize federal property within their boundaries, including forts, customs houses, and arsenals. Several forts, however, remained within Union hands, including Fort Pickens in Pensacola, Florida, and Fort Sumter in Charleston, South Carolina's harbor.