Schools of higher learning were dominated by scholasticism throughout most of the Middle Ages; however, there was an alternative to scholasticism called rationalism. Rationalism was introduced to Europe by the Muslims of Spain. The most important medieval rationalist philosopher was Adelard of Bath (1080-1152 AD).

Rationalism was a secular, non-religious, investigative approach to understanding the world. Scholastics appealed to the authority of Church doctrine and the power of belief to back their claims up; however, rationalists ignored arguments from authority or Church doctrine while claiming if something was true it was true irrespective of authority or belief. Adelard was adamant rationalism was a better tool of investigation when he observed, "Although man is not armed by nature nor is naturally swiftest in flight, yet he has something better by far—reason. The visible universe is subject to quantification, and is so by necessity...between you and me only reason will be the judge...since you proceed according to the rational method, so shall I...I will also give reason and take it..."

The work of Adelard to popularize rationalism (or the use of reason) placed philosophy on an equal footing with religion as being a means of describing the world. In short the rationalists established that nature could by looked at systematically, e.g. Lightning is simply an electrical discharge, etc. rather than through belief, e.g. Lightning strikes therefore Zeus is angry.

In Paris a philosopher named Pierre Abelard (1079-1142 AD) applied rationalism in such a way that it rocked the Church to its foundations. Abelard (shown at right) took the use of reason and logic and applied it to the interpretation of the Bible. For example, in his book Sic et Non (Yes and No), Abelard analysed 168 statements from the Bible and showed that there were inconsistencies in the accepted interpretation of each of them. He compiled all comments made on them, putting arguments for and against each opinion. This technique had been in general use since the time of the early fifth-century Church fathers and was known as the quaestio (the question), in which the pro and contra were compared in order to make judgement. Until the time of Abelard a statement by an accepted authority was sufficient in and of itself as proof enough. Abelard placed arguments from authority in to question.

Though Abelard claimed that his attack on authority aimed only at finding the truth, the Church did not approve. When he said, "By doubting we come to enquiry; by enquiring we perceive the truth," Rome heard the voice of a revolutionary. Abelard laid down four basic rules for argument and investigation:

1). Use systematic doubt and question everything.
2). Learn the difference between statements of rational proof and those merely of persuasion.
3). Be precise in your use of words, and expect precision from others.
4). Watch for error (even in Holy Scriptures).

Statements like these were quite extraordinary in the 12th century. Objectivity, detachment and unprejudiced, unemotional use of reason were rare to the medieval mind, steeped as it was in mystery and dogma. When Martin Luther challenged some of the Catholic Church's teachings three centuries later, he was essentially challenging the Church's authority. Luther, in an appeal to reason, asked Church authorities to show him how he was in error about indulgences. The Church could not; there was no scriptural support for the way the Church was using indulgences—exchanging money for salvation.

Universities by the time of Luther were quickly becoming dominated by Greek rationalism. Also, these centers of higher learning became increasingly independent of Church control (especially in Northern Italy).