This paper aims to reconsider, from the viewpoint of educational ethics, the "religious neutrality of education" that is a fundamental principle of Japan's Basic Act on Education. Religious neutrality in education is a concrete example of the principle of the separation of church and state. The history of the relationship between church and state in the USA and Europe reveals that separation of the two has been enacted in each individual country as a result of a wide range of developments, and could therefore be called a political "product of compromise." The relationship among the three fundamental principles - separation of church and state, freedom of belief, and the spirit of tolerance - can be describedas follows. First, freedom of belief has the definitive meaning of having freedom to follow one's own personal beliefs. However, when this freedom is expanded to mean freedom of belief for both oneself and others, it becomes a right with universal value. What makes such an expansion possible is the spirit of tolerance. For this reason, it can be said that the spirit of tolerance is a condition for freedom of belief, and that the result of the systemization of this spirit of tolerance is the separation of church and state. The separation of church and state thus becomes a means to safeguard freedom of belief. These three elements are inter-related. Tolerance appears to be a universal concept, but it is based on an extremely Protestant philosophy. The same can also be said of freedom of belief, and of the separation of church and state. Moreover, the limits inherent in the separation of church and state are inextricably linked to the limits of religious neutrality in education.