When an inquisitor arrived, a month of grace was allowed to all who wished to confess to heresy and to recant; these were given a light penance, which was intended to confirm their faith. After the period of grace, persons accused of heresy who had not abjured were brought to trial. The defendants were not given the names of their accusers, but they could name their enemies and thus nullify any testimony by these persons. After 1254 the accused had no right to counsel, but those found guilty could appeal to the pope. The trials were conducted secretly in the presence of a representative of the bishop and of a stipulated number of local laymen. Torture of the accused and his witnesses soon became customary and notorious, despite the long-standing papal condemnation of torture (e.g., by Nicholas I); Innocent IV ultimately permitted torture in cases of heresy.

Most trials resulted in a guilty verdict, and the church handed the condemned over to the secular authorities for punishment. Burning at the stake was thought to be the fitting punishment for unrecanted heresy, probably through analogy with the Roman law on treason. However, the burning of heretics was not common in the Middle Ages; the usual punishments were penance, fine, and imprisonment. A verdict of guilty also meant the confiscation of property by the civil ruler, who might turn over part of it to the church. This practice led to graft, blackmail, and simony and also created suspicion of some of the inquests. Generally the inquisitors were eager to receive abjurations of heresy and to avoid trials. Secular rulers came to use the persecution of heresy as a weapon of state, as in the case of the suppression of the Knights Templars.

The Inquisition was an emergency device and was employed mainly in S France, N Italy, and Germany. In 1542, Paul III assigned the medieval Inquisition to the Congregation of the Inquisition, or Holy Office. This institution, which became known as the Roman Inquisition, was intended to combat Protestantism, but it is perhaps best known historically for its condemnation of Galileo. After the Second Vatican Conference, it was replaced (1965) by the Congregation for the Doctrine of the Faith, which governs vigilance in matters of faith.

The Spanish Inquisition was independent of the medieval Inquisition. It was established (1478) by Ferdinand and Isabella with the reluctant approval of Sixtus IV. One of the first and most notorious heads was Tomas de Torquemada. It was entirely controlled by the Spanish kings, and the pope's only hold over it was in naming the inquisitor general. The popes were never reconciled to the institution, which they regarded as usurping a church prerogative.

The purpose of the Spanish Inquisition was to discover and punish converted Jews (and later Muslims) who were insincere. However, soon no Spaniard could feel safe from it; thus, St. Ignatius of Loyola and St. Theresa of Ávila were investigated for heresy. The censorship policy even condemned books approved by the Holy See. The Spanish Inquisition was much harsher, more highly organized, and far freer with the death penalty than the medieval Inquisition; its autos-da-fé became notorious. The Spanish government tried to establish the Inquisition in all its dominions; but in the Spanish Netherlands the local officials did not cooperate, and the inquisitors were chased (1510) out of Naples, apparently with the pope's connivance. The Spanish Inquisition was finally abolished in 1834.

See E. M. Peters, Torture (1985) and Inquisition (1988). For the Spanish Inquisition, see studies by A. S. Tuberville (1932, repr. 1968), C. Roth (1938, repr. 1964), R. E. Greenleaf (1969), P. J. Hauber (1969), H. A. F. Kamen (1965 and 1998), and E. Peters (1989).