In 1896, Shepherd completed his PhD at Columbia University. He then studied in Berlin and finally became professor of history at Columbia University. He is best known for his Historical Atlas, published in several editions during the early twentieth century. He is considered a pioneer in the field of Latin American history. Shepherd's address to the 1909 meeting of the American Historical Association was "probably the first time that a part of the program of the annual meeting was devoted to the history of other peoples in the Americas." In his remarks, he decried that in the United States the history of the western hemisphere focuses on the English colonies and ignores or disparages the history of Spanish, Portuguese, and French America. He called for a more balanced history of the Americas, stressing "That the history of the Spanish, Portuguese, and the French in America possesses an interest and a significance of its own, entirely apart from its relation to the "Anglo-American" element."
- Guide to the Materials for the History of the United States in Spanish Archives. Washington, D.C., Carnegie Institution of Washington, 1907.
- Historical Atlas. New York City, Henry Holt and Company, 1911.
- The Story of New Amsterdam. New York, The Holland Society of New York, 1917.
- The Hispanic Nations of the New World: Our Southern Neighbors. New Haven, Yale University Press, 1919.
- Hispanic Nations of the New World; a chronicle of our southern neighbors, New Haven, Yale University Press, 1921.
- Historical Atlas (Eighth ed.). Henry Holt. 1921.
- Latin America. New York, Henry Holt and Company, 1923.
- Historical Atlas. New York, Henry Holt and Company, 1926.
- Distribution of Races in Austria-Hungary. 1911
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- Lewis Hanke introduction to William R. Shepherd, "The Contribution of the Romance Nations to the History of the Americas" in Latin American History: Essays on its Research and Teaching, 1898-1965 Section III, Pioneers, 1900-1918. Austin: University of Texas Press, 1967, vol. 1, p. 66. Reprinted from Annual Report of the American Historical association for the Year 1909. 1:221-227. Washington DC 1910).
- Shepherd, "The Contribution of Romance Nations", p. 67.
- Works by William Robert Shepherd at Project Gutenberg
- Works by or about William Robert Shepherd at Internet Archive