Using the critical tools of social science, W. E. B. Du Bois challenged the White supremacism of his era. During the late nineteenth and early twentieth centuries, he presented his views on social inquiry in various programmatic pieces (e.g., “The Study of the Negro Problems” and “The Atlanta Conferences”), all the while conducting empirical research on the conditions and experiences of African Americans. This essay examines the ways in which Du Bois's programmatic statements were elaborated in his early works of social science, notably: his goal of scientific truth, the specificity of his research scope, and the research topics for investigation. Three of Du Bois's projects—The Philadelphia Negro; The Negroes of Farmville, Virginia; and the Atlanta University Publications—are detailed. In addition, this essay derives several insights from Du Bois that address issues common to debates in the philosophy of social science, such as the controversies over researcher neutrality and the rigor of politically engaged scholarship.