Geronimo's descendants sued Skull and Bones in 2009 for the skull a member's 1918 letter says was taken from his grave, and a federal judge dismissed the case

Geronimo, a Chiricahua Apache leader, surrendered in 1886 and died a prisoner of war at Fort Sill, Oklahoma, in February 1909. He was buried in the Apache cemetery there. In 1918 Yale army volunteers trained at Fort Sill, Prescott Bush among them. On 7 June 1918 Bonesman Winter Mead wrote to F. Trubee Davison that "the skull of the worthy Geronimo the Terrible" had been exhumed at Fort Sill and was now in the Tomb, the society's New Haven hall. Historian Marc Wortman, who found the letter in 2005, doubts the bones are Geronimo's. In 1986 San Carlos Apache chairman Ned Anderson met Jonathan Bush and the society's lawyer, Endicott Peabody Davison, in New York. Anderson says they showed him bones in a glass case, said tests showed a ten-year-old boy, and asked him to sign a paper stating the society did not have Geronimo. He refused. On 17 February 2009, the centenary of the death, 20 descendants led by Harlyn Geronimo, represented by Ramsey Clark, sued Skull and Bones, Yale, President Obama and the Army. Other descendants intervened to keep the grave undisturbed. On 27 July 2010 Judge Richard Roberts dismissed the suit: the government had not waived sovereign immunity, and NAGPRA's ownership rule covers only remains found on federal land after 16 November 1990. In 2004 a NAGPRA review board member asked the board to investigate. Fort Sill says no evidence supports the claim. Historian David Miller says Geronimo lies intact under concrete at Fort Sill.