The report, which is compiled by the American Medical Association (AMA) with support from the Rockefeller and Carnegie families, decries the inadequacy of American medical schools. It will lead to the closure of almost all Black medical schools.

Over the next decade, the Rockefeller Foundation will fund the General Education Board, financing the reorganization of medical education and patient care. This will further professionalize healthcare by setting up a system of paid faculty who teach in classrooms separate from the hospital itself. These changes will effectively eliminate the apprentice system.

Additionally, the Flexner Report asserts which kinds of medicine can and cannot be proven as "effective." This will lead to the closure of multiple schools of medicine perceived as "illegitimate," including homeopathy and a range of botanical and herbal schools.

Importantly, all but two Black medical schools will be closed, and Black medical school applicants will not be admitted into non-Black programs for the following half century. Flexner writes that Black patients should only be treated by Black physicians due to infectious disease, but the closure of Black medical programs will severely limit the number of Black physicians.