From Viruses, Plagues and History, Page 70:
"But, in spite of the army’s regulations requiring vaccination at the beginning of hostilities and throughout the war, new recruits continuously arrived, mostly from rural farms and cities where vaccination was not regularly given. Neither the Northern nor Southern states had any central authority to make, test, or certify the effectiveness of smallpox vaccines being used. Often the vaccine was inactive or weakened to a degree that it did not give protection. More often, it was contaminated with other microbes. So smallpox outbreaks continued throughout the war. An example was at the battle of Chancellorsville in May 1863, where as many as 5,000 Confederate troops became infected and unfit for duty (29). Similar examples abounded in the Northern army (30,31). In addition, Union and Confederate soldiers who were captured often carried smallpox deep into the South and North, respectively. Alternatively, prisoners developed smallpox afresh in the prison camps. For example, over 2,000 cases of smallpox, with 618 deaths, were recorded among Confederate prisoners of war in the Union prison at Camp Douglas, Illinois, between February 1862 and June 1865. The outbreak at Camp Douglas was a major source of an epidemic in nearby Chicago that lasted for over five years. Of over 600,000 Union and Confederate soldiers, estimates were that 29,000 developed smallpox and over 10,000 died of the disease."

"oments, he was already incubating the smallpox virus. Smallpox was alive and well in Washington, DC in the 1860s, and by 1863, the spread of disease intensified (30). It was said “... scarcely a neighborhood in Washington was free of smallpox.” Lincoln wrote to his older son, Robert, who was in Cambridge, Massachusetts, “... there is a good deal of smallpox here.” The Chicago Tribune reported “... great terror...” in Washington because of smallpox (31). Even before then, smallpox had spread to the White House."

"Returning to Washington by train the afternoon after giving the Gettysburg Address, Lincoln developed a severe headache and fever (31–34). When he arrived back in Washington, the President was placed at bed rest, while complaining of increasing headache, backache, fever and generalized fatigue. Two days later the rash appeared. The diagnosis of smallpox was made, and for the next three weeks Lincoln remained under quarantine at the White House. The case was mild, but upon recovery, Lincoln’s face became pockmarked. His illness lasted slightly less than one month although, like George Washington, he did not recover his full strength until nearly two months later."

"How and where Lincoln became infected are not clear (28,31,34)"