Mobilised at the outbreak of war in 1939, Karski was taken prisoner by the Soviet Army. Two months later, in November, he escaped from a prisoner-of-war camp and returned to the General Government in German-occupied Poland. There he joined the underground Home Army (AK). His knowledge of foreign languages proved to be very useful when he was sent as a courier between the Polish government-in-exile in London and the AK in Poland. As a courier, Karski made several secret trips between France, Britain and Poland.
In 1942 and 1943 Karski reported to the Polish, British and American governments on the tragic situation in Poland and the methodical extermination of the Jews. In order to make his testimony eye-witness, he was smuggled into a death camp in the uniform of a camp guard.
In July 1943, Karski personally reported to president Franklin Roosevelt about this crisis. He also spoke with many other government and civic leaders in the United States, but without success. Most of the people didn't believe him, or supposed that his testimony was much exaggerated war propoganda of the Polish government.
After the war Karski was unable to return to Poland and made his home in the United States and began his studies at Georgetown University, where he received a PhD in 1952. He taught at Georgetown for 40 years in the areas of East European affairs, comparative government and international affairs. In 1954, he became an American citizen after being deprived of his citizenship by Polish communists.
In Story of a Secret State (1944), Karski related his experiences in wartime Poland. In 1985, Karski published The Great Powers and Poland. In 1996, Thomas E. Wood and Stanislaw M. Jankowski published Jan Karski: How One Man Tried to Stop the Holocaust.
After the fall of Communism in Poland, Karski's wartime role was officially acknowledged there. He received the Order of the White Eagle (the highest Polish civil decoration) and the Order Virtuti Militari (the highest military decoration awarded for bravery in combat).
In honour of his efforts on behalf of Polish Jews, Karski was made an honorary citizen of the Israel. In Jerusalem a tree bearing his name was planted in the Alley of the Righteous Among the Nations. Georgetown University, Oregon State University, Baltimore Hebrew College, Hebrew College of America, Warsaw University, Maria Curie-Sklodowska University, and Lodz University have all awarded him honorary doctorates. He died in Washington in July 2000.