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...of the free states and four slaveholding border states that were later joined by pro-Union counties of Virginia (see West Virginia). Republicans opposed the expansion of slavery into territories owned by the United States, which increased Southern desires for secession. However, Republicans (and the previous Democratic administration under Buchanan) rejected any right of secession. Fighting commenced on April 12, 1861, when Confederate forces attacked a United States (federal) military installation at Fort Sumter in South Carolina, the first state to secede.

During the first year, the Union assumed control of the border states and established a naval blockade as both sides raised large armies. In 1862 large, bloody battles such as Shiloh and Antietam were fought, causing massive casualties unprecedented in U.S. military history. A deadly combination of new weapons (including rifles using the Minié ball) and old battlefield tactics such as mass infantry charges led to thousands of casualties per major battle. In September 1862, Lincoln's Emancipation Proclamation made the freeing of slaves in the South a war goal and gave a higher moral cause to the war, despite opposition from Northern Copperheads who tolerated both secession and slavery. The likelihood of intervention from Britain and France, both of which opposed slavery, was thus reduced. In addition, this policy allowed Union armies to liberate enslaved African-Americans, draining a valuable source of manpower from the South. The border states and War Democrats opposed emancipation at first, but gradually accepted it as part of total war needed to save the Union.

In the East, Confederate general Robert E. Lee assumed command of the Army of Northern Virginia and rolled up a series of victories over the Army of the Potomac, but his best general, Thomas Jonathan "Stonewall" Jackson, was killed at the Battle of Chancellorsville in May 1863. Lee's invasion of the North was repulsed at the Battle of Gettysburg in Pennsylvania in July 1863; he barely managed to escape back to Virginia with his badly mauled force. The Union Navy captured the port of New Orleans in 1862, and Ulysses S. Grant seized control of the Mississippi River by capturing Vicksburg, Mississippi in July 1863, thus splitting the Confederacy in two. By 1864, long-term Union advantages in geography, manpower, industry, finance, political organization and transportation were overwhelming the Confederacy. Grant fought a number of bloody battles with Lee in Virginia in the summer of 1864. Lee's defensive tactics resulted in extremely high casualties for Grant's army, but Lee's army was shrinking daily due to casualties and desertions; he was forced to retreat into trenches around his capital, Richmond, Virginia. The stalemate near Petersburg, Virginia presaged the debacle fifty years later in Western Europe (see Trench warfare). Meanwhile, General William Sherman, the leader of the Union Military Division of the Mississippi, captured Atlanta, Georgia and began his March to the Sea, during which he destroyed a hundred-mile-wide swath of Georgia. In 1865, Confederate resistance collapsed after Lee surrendered to Grant at Appomattox Court House.

All slaves in the Confederacy were freed by the Emancipation Proclamation, which stipulated that slaves in Confederate-held areas, but not in border states or in Washington, D.C., were free. Slaves in the border states and Union-controlled parts of the South were freed by state action or by the Thirteenth Amendment, although slavery effectively ended in the U.S. in the spring of 1865. The full restoration of the Union was the work of a highly contentious postwar era known as Reconstruction. The war produced about 970,000 casualties (3% of the population), including approximately 620,000 soldier deaths—two-thirds by disease. The war accounted for more casualties than all other U.S. wars combined. The causes of the war, the reasons for its outcome, and even the name of the war itself are subjects of lingering controversy today. The main results of the war were the restoration and strengthening of the Union (mainly by permanently ending the issue of secession), and the end of slavery in the United States. About 4 million black slaves were freed in 1865. Based on 1860 census figures, 8% of all white males aged 13 to 43 died in the war, including 6% in the North and an extraordinary 18% in the South.

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