In the case of Thomas Young, et al. v. Kirk Fordice et al., 1996, the U.S Supreme Court ruled that Mississippi had not done enough to desegregate its public university system and was still operating an essentially segregated higher education system in violation of federal law. The court held that states have an affirmative duty under the Fourteenth Amendment's Equal Protection Clause to eliminate policies and practices traceable to their prior de jure dual systems which continue to foster segregation in public universities. This includes admission standards, duplication of programs at historically black and white institutions within close geographical proximity, institutional mission assignments etc., even if they may seem neutral on face value but have segregative effects. The ruling emphasized that a state cannot maintain racially identifiable schools unless it can demonstrate no other feasible alternatives exist for achieving diversity without them.

In the dissenting opinion for Thomas Young, et al. v. Kirk Fordice et al., Justice Scalia argued that Mississippi's higher education system was not inherently discriminatory and did not violate the Equal Protection Clause of the Fourteenth Amendment. He contended that while historical racial discrimination had indeed influenced its development, it no longer perpetuated segregation intentionally or in effect. The mere existence of historically black colleges within a state’s university system does not constitute ongoing segregation if students are free to choose where they attend school without any racial restrictions imposed by law or policy. Furthermore, he asserted that federal courts should refrain from dictating educational policies to states unless there is clear evidence of constitutional violations.