Altum est cor hominis et inscrutabile

Although the organized repression of heresy had its foundations in the legislation of the twelfth and early thirteenth centuries, the formal practice of inquisition into heretical depravity was put in place during the pontificate of Gregory IX. The use of the old legal method of inquisitio for the investigation of heresy had been introduced and adapted by Innocent III. Unlike the traditional method of accusatio, which depended on proactive witness testimony, an inquisition allowed the judge to act on his own authority, on the basis of fama. An ideal tool for investigating a hidden crime, it quickly became the normal form of procedure against heresy. Several of the regional councils, in particular those at Narbonne in 1227 and Toulouse in 1229, were central to this process, but the official beginnings of inquisition can be found in the bull Ille humani generis, first issued in 1231, and the decretal Excommunicamus, also of 1231.

In the context of repression, inquisition into heretical depravity, as it was always called, came to embody a highly specialized expertise and developed an impressive documentary tradition that was its ultimate source of power. Each stage of the process of an inquisition produced documentary records, from the initial abjurations and confessions to records of the depositions and the sentences and penances imposed, which were carefully collected and preserved. Together, these records produced a profile of the levels of heresy in a region, and, even if a deponent knew nothing, that fact was still recorded and their statement could be used against them if it later turned out to be false.