On 10 November 1939, the Gestapo arrested Wojciehowski's son, Edmund, as part of German AB-Aktion in Poland, and threatened with execution, as were other representatives of the Polish intelligentsia. Edmund was later released on 4 April 1940 because of Jerzy Antoni Potocki. He was later arrested again on 12 July 1940 because he was one of the 70 Warsaw lawyers who refused remove Jewish associates from the Warsaw Bar Council. The Germans offered his release in exchange for Wojciechowski signing a declaration stating that the Polish government-in-exile was constitutionally illegal. Wojciechowski refused to sign the declaration and Edmund was transferred on 15 August 1940 to the Auschwitz as one of the 1666 people of the first transport from Warsaw, where he soon died of typhus on 23 February 1941. The family received a telegram sent from the concentration camp informing Wojciechowski about his son's passing, and soon an urn of ashes containing the remains of Edmund was sent back to his parents. During the Warsaw Uprising, the ill Wojciechowski along with his wife Maria were rounded up by the Nazis and sent to Durchgangslager 121, a transit camp in Pruszków.