[1] After completing his doctorate in 1910, Estabrook joined the Carnegie Institution, working in the Eugenics Record Office at Cold Spring Harbor.

During his work at Carnegie, he was a special investigator for the Indiana State Commission on Mental Defectives for two years, from 1916 until 1918.

[1] In 1924, Estabrook traveled to Amherst County, Virginia, where he served as an expert witness during the first trial regarding the forced sterilization of Carrie E. Buck.

[1] Estabrook worked at Carnegie in the Eugenics Record Office until 1929, when he joined the American Society for the Control of Cancer.

[4] Estabrook's researched interracial relationships which included mixed race people, Europeans, Africans, and Native Americans in North Carolina.

[5] Estabrook also researched eugenics and sterilization of children with disabilities in Erie County and Buffalo in New York.

[1] The papers of Estabrook are held in the collections of the Indiana State Library,[1] the Carnegie Institution, the American Philosophical Society, and the University at Albany, SUNY.