After the Roman Church had consolidated its power in the early Middle Ages, heretics came to be regarded as enemies of society. The crime of heresy was defined as a deliberate denial of an article of truth of the Catholic faith, and a public and obstinate persistence in that alleged error. At this time, there was a sense of Christian unity among townspeople and rulers alike, and most of them agreed with the Church that heretics seemed to threaten society itself.

However, the repression of heresy remained unorganized, and with the large scale heresies in the 11th and 12th centuries, Pope Gregory IX instituted the papal inquisition in 1231 for the apprehension and trial of heretics. The name Inquisition is derived from the Latin verb inquiro (inquire into). The Inquisitors did not wait for complaints, but sought out persons accused of heresy. Although the Inquisition was created to combat the heretical Cathari and Waldenses, the Inquisition later extended its activity to include witches, diviners, blasphemers, and other sacrilegious persons.

Another reason for Pope Gregory IX's creation of the Inquisition was to bring order and legality to the process of dealing with heresy, since there had been tendencies in the mobs of townspeople to burn alleged heretics without much of a trial. Pope Gregory's original intent for the Inquisition was a court of exception to inquire into and glean the beliefs of those differing from Catholic teaching, and to instruct them in the orthodox doctrine. It was hoped that heretics would see the falsity of their opinion and would return to the Roman Catholic Church. If they persisted in their heresy, however, Pope Gregory, finding it necessary to protect the Catholic community from infection would have suspects handed over to civil authorities since these heretics had violated not only Church law but civil law as well. The secular authorities would apply their own brands of punishment for civil disobedience which, at the time, included burning at the stake.

The inquisitors, or judges of this medieval Inquisition were recruited almost exclusively from the Franscian and Dominican orders. In the early period of the institution, the Inquisitors rode the circuit in search of heretics, but this practice was short lived. The Inquisitors soon acquired the right to summon the suspects from their homes to the Inquisition center. The medieval Inquisition functioned only in a limited way in northern Europe. It was employed most in the south of France and in northern Italy.

Throughout the Inquisition's history, it was rivaled by local ecclesiastical and secular jurisdictions. No matter how determined, no pope succeeded in establishing complete control of the institution. Medieval kings, princes, bishops, and civil authorities wavered between acceptance and resistance of the Inquisition. The institution reached its apex in the second half of the 13th century. During this period, the tribunals were almost entirely free from any authority, including that of the pope. Therefore, it was almost impossible to eradicate abuse.

A second variety of the Inquisition was the infamous Spanish Inquisition, authorized by Pope Sixtus IV in 1478. Pope Sixtus tried to establish harmony between the inquisitors and the ordinaries, but was unable to maintain control of the desires of King Ferdinand V and Queen Isablella. Sixtus agreed to recognize the independence of the Spanish Inquisition. This institution survived to the beginning of the 19th century, and was permanently suppressed by a decree on July 15, 1834.

A third variety of the Inquisition was the Roman Inquisition. Alarmed by the spread of Protestantism and especially by its penetration into Italy, Pope Paul III in 1542 established in Rome the Congregation of the Inquisition. This institution was al so known as the Roman Inquisition and the Holy Office. Six cardinals including Carafa constituted the original inquisition whose powers extended to the whole Church. The "Holy Office" was really a new institution related to the Medieval Inquisition only by vague precedents. More free from Episcopal control than its predecessor, it also conceived of its function differently. Some saw its establishment as an attempt to counterbalance the severe Spanish Inquisition at a time when much of Italy was under Spanish rule. Whereas the medieval Inquisition had focused on popular misconceptions which resulted in the disturbance of public order, the Holy Office was concerned with orthodoxy of a more academic nature, especially as it appeared in the writings of theologians. In its first twelve years, the activities of the Roman Inquisition were relatively modest and were restricted almost exclusively to Italy. Cardinal Carafa became Pope Paul IV in 1555 and immediately urged a vigorous pursuit of "suspects." His snare did not exclude bishops or even cardinals of the Church. Pope Paul IV charged the congregation to draw up a list of books which he felt offended faith or morals. This resulted in the first Index of Forbidden Books (1559). Although succeeding popes tempered the zeal of the Roman Inquisition, many viewed the institution as the customary instrument of papal government used in the regulation of Church order. This was the institution that would later put Galileo on trial.

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