David Starr Jordan founded and participated in many organizations dedicated to the expansion of eugenic thought. 

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In 1909, Jordan led the American Breeder's Association Eugenics Committee, the first explicitly eugenic organization in the United States, as chairman. Jordan later invited Charles Davenport onto the Committee, who would go on to become one of the most influential eugenicists in American history.

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In 1911, the Eugenics Record Office (ERO), perhaps the most influential eugenic organization in the United States, was spearheaded by Davenport, building off of the success of the Committee on Eugenics. Jordan was instrumental in securing funding for this new organization: Jordan used his influence to convince major donors, such as Mary Williamson Harriman, to fund the ERO, emphasizing the importance of eugenic research. The ERO studied the impact of heredity on certain traits and promoted the forced sterilization of unwanted populations. 

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In 1928, Jordan, alongside Paul Popenoe (a former student of Jordan's) and E. S. Gosney, founded the Human Betterment Foundation in Pasadena, California. Founded to teach Americans about the successes of California's eugenic sterilization law, the HBF promoted the expansion of sterilization programs, publishing pamphlets to be used by lawmakers and schools. The HBF gathered statistics about people sterilized by the state to show the eugenic potential of such programs. These statistics were sent to Nazi German officials who used them to promote their own eugenic policy.

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Throughout his life, Jordan served as a kingpin of the American Eugenics Movement: securing funding, building networks, founding organizations, and using his influence and affiliation with Stanford University to promote eugenic policy such as the forced sterilization of disabled people.