The U.S. Supreme Court case Santa Fe Independent School District v. Jane Doe, 1999, revolved around the issue of school-led prayer at high school football games in Texas. The Santa Fe Independent School District allowed student-elected speakers to deliver a public invocation before each game over the public address system. However, several anonymous students and their parents (the Does) filed a lawsuit arguing that this practice violated the Establishment Clause of the First Amendment which prohibits any law respecting an establishment of religion or prohibiting its free exercise thereof. In a 6-3 decision, the Supreme Court ruled in favor of Jane Doe stating that these prayers were indeed unconstitutional as they represented government endorsement and promotion of religion since they took place at school-sponsored events using school facilities under rules established by officials from Santa Fe Independent School District. This ruling emphasized that schools must remain neutral towards religion and cannot endorse religious practices even if initiated by students.

The dissenting opinion in the Santa Fe Independent School District v. Jane Doe case, written by Chief Justice William Rehnquist and joined by Justices Scalia and Thomas, argued that the majority's decision was an unjustified expansion of existing precedents concerning prayer in public schools. They contended that the policy allowing student-led prayers before football games did not constitute government endorsement of religion because it was students who decided whether to have a prayer and who should lead it. The dissenters believed this policy merely provided a forum for free speech without endorsing any particular message or viewpoint. They also criticized the majority's reliance on perceived coercion, arguing that peer pressure does not equate to governmental coercion into religious conformity.