The Inquisition was a judicial instrument of the Church during the Middle Ages. The purpose of the Inquisition was to combat devil-worship, adultery, incest, and especially heretics and heresy (particularly Cathars and Waldensians). The Inquisition actively sought offenders and put them to trial. In the eleventh century, the Cathar faith spread across Europe. For the duration of that century and in the next, there were few institutional checks on the spread of heresy. By 1150, the Church began to feel threatened by the numbers of heretics, which continued to grow despite the fact that the Second Lateran Council of 1139 had required the civil authorities to prosecute heretics. Pope Lucius III (1181-1185) tried in vain to encourage secular rulers to punish heretics. Finally, in 1231, Pope Gregory IX (1227-1241) launched the Inquisition and directed that secular punishment be inflicted on those condemned by the Church.

An official sent out as an agent of the Inquisition was called an Inquisitor, a position of high honour. Initially, their presence, and that of the Inquisition itself, were resented by the local people and rulers. However, the civil authorities, under threat of excommunication, finally accepted the new situation and the Inquisition was entrenched by 1255. When the Inquisition arrived in a city or town, a "Time of Grace", usually thirty days would be granted, during which heretics had an opportunity to confess and avoid prosecution if they revealed the names of their fellow heretics. After the "Time of Grace", suspects who had not yet confessed to heresy were summoned to the Inquisitor, and he would decide whether or not the suspect was a heretic. Only two witnesses were necessary to make an accusation. The suspect was not told the names of his accusers, for fear that he would later take revenge upon them, but was allowed to draw up a list of his enemies. The Inquisitor was to discount any testimony given by those on the list.

The penalties for lesser acts of heresy included prayer, fasting, charity, flogging and pilgrimages. For serious acts of heresy, the offender was forced to ear the yellow cross, could be imprisoned or have his property confiscated. Heretics who would not repent, or habitually returned to heresy, might be executed by secular authorities. This punishment was not common. By the end of the thirteenth century, the power of the Inquisition had declined except in Spain and Portugal, owing to the Great Western Schism and its won effectiveness in repressing the Cathar threat.

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