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From the National Archives:

The Case of Dr. Samuel Mudd

On April 15, 1865, Dr. Samuel Mudd set the leg and allowed President Lincoln’s assassin John Wilkes Booth and his accomplice David Herold  sleep at his house.  Dr. Mudd was convicted of conspiring to help Booth escape because he did not alert the authorities to Booth’s presence at his farm.  He was given a life sentence, but was pardoned by President Andrew Johnson on February 8, 1869 following his leadership and heroic action to help the sick during a yellow fever epidemic at Fort Jefferson where he was imprisoned.

Dr. Mudd’s grandson Dr. Richard Mudd worked hard to clear his grandfather’s of complicity in the assassination.  He petitioned President Jimmy Carter who sent this reply on July 24, 1979.  

"…Your petition and the petitions submitted to me on behalf of your grandfather by numerous members of Congress, several state legislatures, historians and private citizens have been exhaustively considered by my staff over the past two years.  Regrettably, I am advised that the findings of guilt and the sentence of the military commission that tried Dr. Mudd in 1865 are binding and conclusive judgement, and that there is no authority under law by which I, as President, could set aside his conviction.  All legal authority vested in the President to act in this case was exercised when President Andrew Johnson granted Dr. Mudd a full and unconditional pardon on February 8, 1869."

Read more documents about Dr. Samuel Mudd at the Jimmy Carter Library.