His dissertation, entitled Heredity and Sexual Influences In Meristic Variation: A Study of Digital Malformations in Man, was published in 1903.

[4] The bulk of his research was regarding a hereditary conditions that primarily afflicts the hands of individuals, entitled Brachydactyly.

[5] For his dissertation research, Farabee chose a family affected by this trait and followed their pedigree back five generations.

His goal was to record the cultural diversity and obtain items for the Penn Museum of Archaeology and Anthropology in Philadelphia, where he was employed as a researcher and curator.

[7] The notes taken by Farabee were regarding the many different aspects of the cultures he encountered, such as dance, cosmology, marriage, dress, and particularly their varying languages.

The ethnologies followed a set outline of characteristics to record, but in spite of this there is a great deal of personal detail and rich account of the people.

His array of pottery, beadwork, clothing, ornaments and other artifacts represent an amazing cultural diversity.

The volumes that Farabee produced from his travels include Indian Tribes of Eastern Peru based on his first trip in 1906–1908.

He did not produce any doctorates in physical anthropology during his time teaching at Harvard, which has earned him some criticism, there may be political reasons for this.

While Farabee was more interested in research than teaching, and may not have attracted students for this reason, it has been noted that Putnam may have also had a stifling effect on the department at the time.

[11] In addition to the lack of students, Farabee also faced personal insults in print, such as those he presented in a rebuttal,[12] when he was criticized for his report on the Arawak people.

President Hastings selected his as a member of the American Commission to the Peruvian Centennial with the rank of Envoy Extraordinary.