W. E. B. Du Bois served on the board of Sanger's Harlem clinic.
Sanger believed that lighter-skinned races were superior to darker-skinned races, but would not tolerate bigotry among her staff, nor any refusal to work within interracial projects. Although Sanger's views on race appear archaic from a modern viewpoint, her contemporaries in the African-American community supported her efforts. In 1929, James H. Hubert, a black social worker and leader of New York's Urban League, asked Sanger to open a clinic in Harlem. Sanger secured funding from the Julius Rosenwald Fund and opened the clinic, staffed with African-American doctors, in 1930. The clinic was directed by a 15-member advisory board consisting of African-American doctors, nurses, clergy, journalists, and social workers. The clinic was publicized in the African-American press and African-American churches, and received the approval of W. E. B. Du Bois, founder of the NAACP. Sanger's work with minorities earned praise from Martin Luther King, Jr., in his 1966 acceptance speech for the Margaret Sanger award.
From 1939 to 1942 Sanger was an honorary delegate of the Birth Control Federation of America, which included a supervisory role – alongside Mary Lasker and Clarence Gamble – in the Negro Project, an effort to deliver birth control to poor African Americans. Sanger wanted the Negro Project to include black ministers in leadership roles, but other supervisors did not. To emphasize the benefits of involving black community leaders, she wrote to Gamble "we do not want word to go out that we want to exterminate the Negro population and the minister is the man who can straighten out that idea if it ever occurs to any of their more rebellious members." This quote has been used by numerous Sanger detractors, including Angela Davis and the pro-life movement, to support their claims that Sanger was racist. However, according to New York University's Margaret Sanger Papers Project, Sanger, in writing that letter, "recognized that elements within the black community might mistakenly associate the Negro Project with racist sterilization campaigns in the Jim Crow South, unless clergy and other community leaders spread the word that the Project had a humanitarian aim."