Lexington in the American Civil War Lexington , Kentucky was a city of importance during the American Civil War , with notable residents participating on both sides of the conflict . These included John C . Breckinridge , Confederate generals John Hunt Morgan and Basil W . Duke , and the Todd family , who mostly served the Confederacy although one , Mary Todd Lincoln , was the first lady of the United States , wife of President Abraham Lincoln . Prominent families . Among the well known of Lexington ' s families were the Todds . Abraham Lincoln ' s wife Mary Todd Lincoln was born there on December 13 , 1818 . She left in 1839 from the family home to live with her sister in Springfield , Illinois , where she would meet Abraham Lincoln in 1842 . She went back to Lexington in 1847 to introduce her family to Lincoln on their way to Washington , D . C . for Lincoln ' s one term as Congressman . The Lincolns returned twice more to the city in 1849 and 1850 , the latter to cope with the death of a son . The Todd family was split apart by the war . Mary ' s father Richard Smith Todd had fourteen children , of whom six chose the Union side , while eight others went for the Confederacy . Save for Levi Todd , the Todds that remained in Lexington during the war were pro - Confederate , and did not hide their preference . Also affected were the Breckinridges and Clays . Robert J . Breckinridge was called " the strongest and sturdiest champion of the Union south of the Ohio " . However his nephew John C . Breckinridge , Vice President of the United States under Lincoln ' s predecessor James Buchanan , two of his sons ( Willie and Robert Jr . ) , and a son - in law joined the Confederacy . Of Henry Clay seven grandsons , three sided with the North , and four went for the South . The Morgans , on the other hand , were in one mind and were sympathetic to the Confederacy . 1860 – 1862 . Lexington was preparing for the war even before Lincoln ' s election . When Kentucky governor Beriah Magoffin established pro - Southern Home Guards in March 1860 , the Lexington Rifles were the first to join . When Lincoln was elected President , United States flag stopped being displayed in the city . When news of the Battle of Fort Sumter reached Lexington , the leader of the Lexington Rifles , John Hunt Morgan , telegraphed Confederate President Jefferson Davis to offer assistance , and raised the Confederate flag above the city ' s woolen factory . The first conflict in Lexington took place in August 1861 . Union cavalry arrived in the city on August 21 , numbering 200 . Lexington Home Guard with Confederate sympathies quickly arrived on the scene . Former United States Vice President John C . Breckinridge , a resident of the city , negotiated between the Union cavalry and Confederate home guard , allowing the cavalry to safely depart the city . On September 19 a strong Union force returned the city , with orders to disarm the home guard . Then Captain John Hunt Morgan led Confederate sympathizers from the city , to rendezvous with other Confederates by the Green River . The Union force would make the city a stronghold , and established a prison and hospital in the town . The Confederates would return to the city following the Battle of Richmond . On September 2 , 1862 , Major General Edmund Kirby Smith led 11 , 000 Confederate soldiers into the city , discovering that Union forces had destroyed their ( Union ) government stores before skedaddling from the city . The residents of Lexington cheered the boys in gray , prompting Smith to cable the Confederate government , saying , " They have proven to us that the heart of Kentucky is with the South in this struggle . " Following the Battle of Perryville , the Confederates left the city on October 8 , with Union forces returning on October 16 . However , on October 18 Morgan had returned to Lexington and captured Union Major Charles B . Seidel at Ashland , the former home of Henry Clay . Morgan reequipped his men , destroyed the military supplies of the city , and left . However , during the short firefight , the Confederates had managed to fire on other Confederates , causing John Hunt Morgan ' s brother Wash to be mortally wounded . Wash Morgan was taken to the Morgan family home of Hopemont to die . 1863 – 1865 . In the first three months of 1863 , war refugees sympathetic to the Union arrived in the city . These mostly consisted of whites from eastern Tennessee , and escaped slaves . Morgan made his last return to the city on June 8 , 1864 . Having lost his better soldiers in the previous year ' s Morgan ' s Raid , these men proceeded to loot the city . At least $ 13 , 000 in varied monies and $ 25 , 000 of horses were taken , with clothing stores looted as well . Morgan left for Cynthiana , Kentucky , where he was defeated , causing him to leave Kentucky for Virginia . Morgan was killed in Greenville , Tennessee the following September . In February 1865 John C . Breckinridge was selected to be the Secretary of War . At the end of the war he left the country until given amnesty in 1868 . Aftermath . In 1868 John Hunt Morgan was reinterred in Lexington Cemetery . Including his brother - in - law Basil W . Duke , they are two of seven Civil War generals buried in the cemetery . There are four monuments to the Confederacy located in Lexington . Two are by the old courthouse : the John Hunt Morgan Memorial ( 1911 ) and the John C . Breckinridge Memorial ( 1887 ) . The other two are in Lexington Cemetery : the Confederate Soldier Monument in Lexington ( 1893 ) and the Ladies ' Confederate Memorial ( 1874 ) . There are no monuments to the Union in Lexington , unlike Louisville , where only one of the four monuments is for Confederates .