The question of school-sponsored prayer has proven highly controversial.  In the landmark case of Engel v Vitale in 1962, the Court ruled that New York's practice of beginning school days with a prayer drafted by school officials violated the Establishment Clause.  This is the case, the Court said, whether or not students are given the option of not participating in the prayer.  Writing for the Court, Justice Black said the Establishment Clause was violated when school put "indirect coercive pressure upon religious minorities to conform to the officially approved religion."  Peer pressure being as strong as it is among the young, many students who might otherwise choose not to participate in prayer will do so for fear of  otherwise being seeing as an oddball.

Engel dealt with an officially approved prayer, not the question of whether school officials could set aside time for voluntary silent prayer.  That issue arose in the 1985 case of Wallace v Jaffree.  Alabama had for some time authorized schools to dedicate part of the school day for "a period of silence for meditation."  The period-of-silence law almost certainly did not offend the First Amendment because it did not endorse religious reflection over other types of reflection, be they philosophical or personal.  Not satisfied, it seems, with how students might be using their period of silence, Alabama legislators amended the statute to provide for a "period of silence for meditation or silent prayer."  The sponsor of the legislation frankly stated that the purpose of his amendment was to get more kids to use their time to recite prayers.  In Wallace, the Court, voting 5 to 4, held that the amendment to the Alabama moment-of-silence law lacked a secular purpose and struck it down. 

Lee v Weisman (1992) considered school prayer in the special context of a graduation ceremony for a middle school.  The principal of the school had invited a clergyman to offer an invocation and benediction at the ceremony, and that decision was challenged by Weisman, who contended that the practice violated Establishment Clause precedents.  Again voting 5 to 4, with Justice Kennedy providing the key vote, the Court found the invocation and benediction to violate the First Amendment.  Kennedy found an unacceptable degree of coercion, given the fact that the ceremony was an important milestone that students would be extremely reluctant to avoid because of religious scruples.  The options of remaining seated during prayers or leaving right before the benediction did not seem realistic under the circumstances.  Justice Scalia, in a passionate dissent, ridiculed Kennedy's opinion as a "psycho journey" and wrote that he would not find a problem with prayer at graduation ceremonies unless the state attached a penalty to non-participation.

In general, the Court has demonstrated a willingness to strike down any practices that might be likely to be perceived either as coercive or as a state endorsement of religion.  That trend continued with the Court's Santa Fe v Doe decision in 2000, which considered the policy of a Texas school district that allowed students to elect students to speak briefly over the PA system before high school football games.  Traditionally, the speeches were religious in character--the policy stated that the speeches should solemnize the event and be nonsectarian in nature.  The Court found the Santa Fe school policy to be a violation of the Establishment Clause.  The Court reasoned that the speeches were at a school-sponsored event, using school facilities, and would be taken by most observers as a school endorsement of the student prayers that were likely to be delivered.  The election process ensured, the Court thought, that the religious messages would reflect the religious views of the majority of Students, who in the case were generally Fundamentalist Christians.  The three dissenters argued that the school policy was neutral on its face and not a constitutional violation.  Nothing in the school policy, the dissenters said, even required that the message be religious in nature.