1. Origins

The Inquisition was never a pan-Christian movement – it was always a specific Roman Catholic institution. That being the case, Protestants hold no blame for its actions. The Inquisition began in the 12th century as a result of the quasi-Gnostic Cathar (Albigensian) heresy in Provence (France). A Crusade was called against the Cathars, and linked to this, was the need to expose heresy and heretics, convert and if necessary, punish them through secular means – imprisonment and execution. In the NT, heresy and apostasy are only punishable by excommunication. Henry Charles Lea, A History of the Inquisition of the Middle Ages, Vol. 1 (New York: Cambridge University Press, 2010, originally published 1888), p. 307, presents the origins of the Inquisition:

In 1204 Gui, Archbishop of Reims, summoned Count Robert, cousin of Philip Augustus, the Countess Yolande, and many other laymen and ecclesiastics to sit in judgment on some heretics discovered at Brienne, with the result of burning the unfortunate wretches. In 1201, when the Knight Everard of Chateauneuf was accused of Catharism by Bishop Hugues of Nevers, the Legate Octavian summoned for his trial at Paris a council composed of archbishops, bishops, and masters of the university, who condemned him.

Later, the Papacy organised a more systematic means of enforcing uniformity (p. 320): ‘Innocent III endeavored, at the Lateran Council of 1215, to secure uniformity by a series of severe regulations defining the attitude of the Church to heretics, and the duties which the secular power owed to exterminate them under pain of forfeiture, and this became a recognized part of canon law..’ It was under Pope Honorius III that the system became more firmly established (p. 321):

In a series of edicts dating from 1220 to 1239 he thus enacted a complete and pitiless code of persecution, based upon the Lateran canons. Those who were merely suspected of heresy were required to purge themselves at command of the Church, under penalty of being deprived of civil rights and placed under the imperial ban; while, if they remained in this condition for a year, they were to be condemned as heretics. Heretics of all sects were outlawed; and when condemned as such by the Church they were to be delivered to the secular arm to be burned. If, through fear of death, they recanted, they were to be thrust in prison for life, there to perform penance. If they relapsed into error, thus showing that their conversion had been fictitious, they were to be put to death. All the property of the heretic was confiscated and his heirs disinherited. His children, to the second generation, were declared ineligible to any positions of emolument or dignity, unless they should win mercy by betraying their father or some other heretic. All “credentes,” fautors, defenders, receivers, or advocates of heretics were banished forever, their property confiscated, and their descendants subjected to the same disabilities as those of heretics. Those who defended the errors of heretics were to be treated as heretics unless, on admonition, they mended their ways. The houses of heretics and their receivers were to be destroyed, never to be rebuilt. Although the evidence of a heretic was not receivable in court, yet an exception was made in favor of the faith, and it was to be held good against another heretic. All rulers and magistrates, present or future, were required to swear to exterminate with their utmost ability all whom the Church might designate as heretics, under pain of forfeiture of office.

We should conceptually distinguish the Episcopal and the later Papal Inquisitions (Michael C. Thomsett, The Inquisition: A History, [Jefferson & London: McFarland & Company, Inc., 2010], p. 13):

Pope Lucius III (1181–5) declared the Episcopal Inquisition on November 4, 1184, through his papal bull Ad abolendum (On Abolition). Also referred to as the Charter of the Inquisition, the bull stated the pope’s intention:

To abolish the malignity of diverse heresies which are lately sprung up in most parts of the world, it is but fitting that the power committed to the church should be awakened, that by the concurring assistance of the Imperial strength, both the insolence and mal-pertness of the heretics in their false designs may be crushed, and the truth of Catholic simplicity shining forth in the holy church, may demonstrate her pure and free from the execrableness of their false doctrines…. [W]e likewise declare all entertainers and defenders of the said heretics, and those that have showed any favor or given countenance to them, thereby strengthening them in their heresy, whether they be called comforted, believers, or perfect, or with whatsoever superstitious name they disguise themselves, to be liable to the same sentence…. And as for a layman who shall be found guilty either publicly or privately of any of the aforesaid crimes, unless by abjuring his heresy and making satisfaction he immediately return to the orthodox faith, we decree him to be left to the sentence of the secular judge, to receive condign [deserved] punishment according to the quality of the offense…. [B]ut those who after having abjured their errors, or cleared themselves upon examination to their bishop, if they be found to have relapsed into their abjured heresy—We decree that without any further hearing they be forthwith delivered up to the secular power, and their goods confiscated to the use of the church.

This bull specifically instructed bishops to turn unrepentant heretics over to civil authorities for punishment.

Pope Gregory IX established the Papal Inquisition in 1231 (p. 28):

In the same year, Gregory established the formal Papal Inquisition. Unsatisfied with the progress made toward stamping out heresy, Gregory took away from Church bishops the authority to manage punishment, and claimed it to be within the pope’s authority to set rules. Thus, the Medieval Inquisition replaced the earlier, less formal Episcopal Inquisition that had been established by Lucius III. The failure of the Episcopal Inquisition influenced Gregory’s decision to create a more encompassing Inquisition under the control of the papacy itself. He determined to staff investigations with professionals, primarily from the Dominican Order. Gregory’s Inquisition had an organized, systematic character and was far more effective in gaining the desired result, the punishment of heretics.

Thus, it can be seen that the original aim of the Inquisition was to extirpate heresy, not Islam or Judaism. Therefore, when the Reformation came, the Inquisition was used against Protestants, since the Papacy – and thus the Inquisition – saw them as heretics.

  • First Victims

The first victims were Cathars, who held to a form of Gnosticism. Another early victim was the Waldensian sect, essentially a proto-Protestant group (pp. 14-15):

Among the targets of the initial Episcopal Inquisition enacted by Lucius III were the Waldensians. This was a movement that began in about 1177 in Italy, based on the beliefs of Peter Waldo…

Among the important theological differences between the Waldensians and the Church was the former’s refusal to accept the concept of purgatory (purgare, meaning to make clean), since it is not mentioned in the Bible. They also refused to venerate the saints. Perhaps most offensive to the Church, the Waldensians believed that anyone, not only priests, had the right to consecrate sacramental bread and wine. In short, the Waldensians thought of the Churchas unbiblical in much of its dogma.

Waldensians also refused to swear oaths, so that in a tribunal aimed at presenting evidence of heresy, a member of this sect was treated as a suspect refusing to tell the truth. Both Church and secular authorities were troubled as well by the Waldensians’ refusal to go to war.

Hence, even though they posed no military threat to the Papacy or the State, they were condemned and persecuted by the Inquisition. Another group were alleged witches, p. 15: ‘The Waldensians were later accused of practicing witchcraft and were among those persecuted in Europe’s Great Witch Hunt (1450–1750), a variant of the Inquisition focused on witches as heretics.’ As witch-fever mounted, the Papacy acted (p. 97):

It has indeed lately come to Our ears, not without afflicting Us with bitter sorrow, that in some parts of Northern Germany … many persons of both sexes, unmindful of their own salvation and straying from the Catholic Faith, have abandoned themselves to devils, incubi and succubi, and by their incantations, spells, conjurations, and other accursed charms and crafts, enormities and horrid offences, have slain infants yet in the mother’s womb, as also the offspring of cattle.

—Pope Innocent VIII, papal bull Summis desiderantes affectibus, December 5, 1484

Sometimes, witches were treated leniently – notably (if somewhat ironically) in Spain (p. 101):

In Spain in the mid-period of the Great Witch Hunt, Inquisition tribunals were far more lenient than in the rest of Europe. This may seem to contradict the history of the Inquisition’s harshness against other groups, notably converted 

Jews and Lutherans. In Spain, as elsewhere, accused witches told fantastic tales of their supernatural exploits, stories brought out under torture or the threat of it. But the inquisitor in Saragossa, Pedro Ciruelo, had an explanation. He believed that the stories inquisitors were hearing came from pacts entered with the devil, but that people entered these pacts as the result of ignorance and superstition. Ciruelo urged leniency toward accused witches.

Other times and elsewhere, they felt the full wrath of the Inquisition (p. 102): 

In 1427, Franciscan missionary and preacher Bernardino da Siena campaigned against baby killers and witches, whom he termed “devilish women” (femmine indiavolate). He encouraged his listeners to denounce witchcraft and to show no sympathy for witches, asking how they would feel if a witch had murdered one of their children. He asked that anyone who suspected another of being a witch report them at once to the Inquisition. The denunciations soon began in large numbers. A trend began, in which those accused of the most fantastic crimes were most likely to be found guilty and burned at the stake.

Other groups attacked by the Inquisition included the proto-Protestant John Wyclif’s followers in England – the Lollards (p. 91):

Although Wyclif died at the end of 1384, he remained a problem for the Church for many years to follow. In 1401, an anti–Wyclif statute was extended to the Lollards by Parliament, condemning Wyclif and his followers. The statute, De hæretico comburendo (The Burning of Heretics), described the Lollards:

And of such sect and wicked doctrine and opinions, they make unlawful conventicles and confederacies, they hold and exercise schools, they make and write books, they do wickedly instruct and inform people, and, as much as they may, excite and stir them to sedition and insurrection, and make great strife and division among the people, and do daily perpetrate and commit other enormities horrible to be heard, in subversion of the said Catholic faith and doctrine of the Holy Church,

in diminution of God’s honor, and also in destruction of the estate, rights, and liberties of the said English Church; by which sect and wicked and false preachings, doctrines, and opinions of the said false and perverse people, not only the greatest peril of souls, but also many more other hurts, slanders, and perils, which God forbid, might come to this realm….

In 1408, the Constitutions of Oxford banned all of Wyclif ’s writings, especially his late-life translation of the Bible into English.

Later, the attack on heresy in England became legally formalised (p. 92):

In the decades after Wyclif ’s death, Lollards were brought before the tribunals of the Inquisition and an active crusade was initiated against them. Many recanted but many more were found guilty of heresy and executed. Heresy trials in England had been rare up until this time, but the Lollards were of special interest to the inquisitors. The movement had gained in popularity in spite of persecution. One writer of the day claimed that out of every two men encountered on the road, one was sure to be a Lollard.

In 1401, Henry IV became King of England and under his rule a new policy was undertaken in dealing with the Lollards. Parliament passed an act the same year legalizing the burning of heretics, the first law of its kind in England, which led to executions of hundreds of accused heretics. This law outlawed preaching, teaching or publishing by Lollards; offenders were to be tried by courts of the local diocese and upon being found guilty, handed over to civil authorities and burned at the stake.

In Bohemia (present-day Czech Republic), Jan Hus, a follower of Wyclif, was condemned by the Pope, and his supporters were persecuted (p. 93): ‘When followers of Hus expressed their view agreeing with Hus that indulgences were improper, they were beheaded, becoming the first martyrs in what came to be known as the Hussite Church.’ Hus himself was burnt, and we should note what the death-sentence involved as to terminology (pp. 94, 95): ‘ The ritual continued; a paper hat was placed on his head with the inscription Hæresiarcha (leader of a heresy) and a drawing of the devil. He was then delivered under guard to the local secular authorities with the order, “Take him and do to him as a heretic.”… Then the fire was lit.’ Note what was stated: ‘do to him as a heretic’. It follows that the initial emphasis of the Inquisition was on heresy, not Judaism or Islam, and burning people was originally the punishment of a heretic. 

  • Spain under Islam

Islam did not arrive in the Iberian Peninsula as a missionary faith, but rather as a political conqueror. It began in 711 (Roger Collins, Early Medieval Spain: Unity in Diversity, 400-1000, [Basingstoke & London: Macmillan Education Ltd, 1983], p. 151):

Essentially, the Arab conquest of Spain seems to have developed along the following lines: after the military subjugation of most of North Africa had been completed, but long before the cultural and religious assimilation of its indigenous Berber inhabitants can have occurred, an expedition, probably originally intended as a probing raid, was sent into Spain in 711 by Musa ibn Nusayr, the Arab governor of Ifrikiya (the new Arab North Africa), under the command of his former slave Tarik.

Thereafter the conquest continued so that within a few years most of the Peninsula was under Islamic rule (Joseph F. O’Callaghan, Reconquest and crusade in medieval Spain, [Philadelphia: University of Pennsylvania Press, 2003], p. 1):

From 711, when a mixed force of Arabs and Moroccan Berbers crossed the Strait of Gibraltar and overthrew the Visigothic kingdom, until the collapse of the Umayyad Caliphate of Cordoba in 1031, Muslim supremacy in Spain was unquestioned. As the seat of Islamic power was Cordoba, an eccentric location in the southern part of the peninsula, the Muslims did not permanently occupy large stretches of mountainous zones in the north. That made it possible for small groups of Christians to form the tiny, independent states of Asturias, Leon, Castile, Navarre, Aragon, and Catalonia. Clinging to the Cantabrian and Pyrenees mountains, this congeries of Christian enclaves, variously ruled by kings or counts, was kept on the defensive for nearly three hundred years, as Muslim armies marched northward every summer to ravage their lands but never to conquer them. 

The treatment of non-Muslims was based on subjugation, especially of the Catholics (Collins, Early Medieval Spain, p. 203):

New synagogues were built, such as the one founded in Cordoba by Hasdai ibn Shaprut’s father Isaac, while a ban existed on the erection of Christian churches. Like the Christians, the Jews were obliged, as non-Muslims, to wear distinctive dress, and both groups were forbidden, by a survival of principles from earlier Roman and Visigothic legislation, to own Muslim slaves. Their other slaves could in theory obtain liberty by embracing Islam, but it is tempting to wonder if the difficulties of applying these rulings in practice differed appreciably from those of earlier centuries.

Other restrictions were made (p. 207): ‘They were forbidden to build new churches or to advertise their worship by the ringing of bells…’ Islamic law was State law, and blasphemy was severely punished (Darío Fernández-Morera, The Myth of the Andalusian Paradise: Muslims, Christians, and Jews under Islamic Rule in Medieval Spain[Wilmington: ISI Books, 2016], pp. 102-103):

In Umayyad Córdoba, Maliki authority Uthman ibn Kinana (d. 802) asserted that a ruler could choose what kind of punishment to administer for blasphemy, either beheading or crucifixion. The few documents that have reached us confirm the application of these penalties. The qadi (judge) Said ibn Sulayman al-Balluti agreed that death must be dealt to a blasphemer. In Umayyad Córdoba between 961 and 976, the ulama condemned to death a man, Abu al-Hayr, for insulting the Companions of the Prophet publicly and saying that one should be allowed to drink wine (something expressly prohibited, as we will see). Earlier, in 919, a Córdoban qadi prescribed death for a Christian female dhimmi guilty of saying publicly that Jesus was God and Muhammad a false prophet. In 1064, in Muslim-ruled Toledo, a Muslim man was crucified for blasphemy at the entrance to the city’s main bridge. 

In the History of the Judges of Córdoba, al-Khushani gives another instructive example under Umayyad ruler Abd al-Rahman II in the mid-ninth century. Abd al-Rahman removed a judge for prescribing a punishment less strict than death against a Muslim man accused of uttering words offensive to Allah—blasphemy. The ruler then named a new judge, who had the impious man suffer the death prescribed by Maliki jurisprudence: crucifixion. While being placed on the cross, the blasphemer shouted that he was innocent and that he did believe after all that there was no other God but Allah and that Muhammad was indeed His Prophet, but this repentance did not stop his crucifixion. 

An extant account of the punishment of an alim accused of blasphemy under Abd al-Rahman II indicates that in Islamic Spain a blasphemer could be both crucified and stabbed on the cross, a curious combination that was in fact proper according to Maliki doctrine. To be sure, as in Catholic Spain, the authorities could finesse what constituted blasphemy in view of their interests of the moment, and a blasphemer might be given the opportunity to recant and be guided back to the straight path. A blasphemer’s life, however, remained always at serious risk in al-Andalus.

Heresy and apostasy were also capital crimes (Ibid.):

Heresy also was punishable with death, though circumstances, or a ruler’s intervention, could save the occasional alim suspected of heresy. Al-Khushani records that a favorite of the Umayyad ruler Muhammad I (reigned 852–886) was accused of holding heretical views. The Córdoban fuqaha decided that this heretic deserved death “to extirpate the bad effects that his ideas would cause.” The only way Muhammad I found to save his favorite was to remove the judge before whom the case was being argued, thereby nullifying the judicial process, which then died out through legal inertia.

Islamic law treatises used even by Muslims under Christian domination prescribed death for a Muslim who, after three days in jail, still did not repent from his heresy; after he was killed, his property went to the community. In these treatises, apostasy and blasphemy were even worse than heresy: if a Muslim practiced another religion in secret, he must be killed and no attention must be given to his denials or his vows of repentance; a Muslim who offended Allah must be killed; whoever insulted the Prophet Muhammad must be killed and no repentance was acceptable.

Along with other restrictions, such as the Jizya, it is clear that Muslim Andalusia was no Paradise for the native Catholic inhabitants (Kenneth Baxter Wolf, Christian martyrs in Muslim Spain. [Cambridge & New York: Cambridge University Press, 1988], pp. 11-12):

The Christians of Cordoba were without a doubt subject to regular taxation. Eulogius complained of a “monthly tribute” that constituted a financial hardship for the Christians. Similarly Alvarus wrote of an “unbearable tax” that weighed heavily on Christian necks. There is little doubt, given the tone of victimization that both men adopted when speaking of the levies and the regularity with which they were collected, that tributum, vectigal, and census were simply Latin synonyms for the universal dhimmz tax, the Jizya.

The Cordoban authorities also prosecuted Christians guilty of blasphemy. In the spring of 850, a priest named Perfectus was arrested and later executed for publicly expressing his opinions about the errors of Islam to a group of Muslims. Months later a Christian merchant named Joannes suffered a severe lashing, public humiliation, and a long prison term for invoking the prophet’s name as he sold his wares in the marketplace.

Clearly, the laws regarding blasphemy were enforced with vigour against the native Catholics by the conquering Muslims.

  • Spain under Reconquista and Inquisition

From the eleventh century, the Muslim dominance of the Peninsula began to recede, and the re-conquest (Reconquista) began, completed in 1492 with the fall of the last Muslim emirate, Granada. During the era of Islamic domination, many Catholics had converted to Islam, usually to avoid the Jizya and to gain social preference (as elsewhere in Dar al-Islam). The Catholic rulers – and the Catholic Church – were determined to win these ‘back’ to the Papal obedience (although by then, we are speaking of the descendants of the original converts). Roman Catholic policies were already negative towards Judaism, but the idea, though perhaps exaggerated, the Jews had been favoured by the Muslims above Catholics intensified hostility. At any rate, the Catholic rulers were determined to have a monolithic Catholic populace, either by expulsion of Jews and Muslims, or their conversion. The problem for the Catholics, is that many Jews and Muslims merely feigned conversion (Conversos and Moriscos), but secretly practised their old faiths. Hence the Inquisition (Thomsett, The Inquisition: A History, p. 147): ‘Two years after Spain’s King Enrique IV requested that the pope establish a new Inquisition, Pope Pius II (1458–64) complied. The overall purpose of this new Inquisition was to investigate instances of heresy among the Conversos of Spain.’ 

The Inquisition began to accelerate in action and scope under Queen Isabella of Castile, and her husband, Ferdinand of Aragon (p. 149):

In 1478, after repeated requests from Hojeda and other anti–Conversos, Isabella and Ferdinand asked Pope Sixtus IV (1471–84) to issue a papal bull to establish a new Inquisition. On November 1, 1478, Sixtus issued his bull, Exigit sinceras devotionis affectus, creating the new Inquisition to be based in Castile. Terms of this new Inquisition included a ruling that three priests were to be appointed to a tribunal, with their selection left up to the royal couple as Ferdinand and Isabella had insisted. In 1480, the first tribunal was established, consisting of royal appointees of two Dominicans, Juan de San Martín and Miguel de Morillo, as well as Juan Ruiz de Medina as adviser. Allegations of Converso plots to arm and assault or assassinate the inquisitors led to numerous arrests and the convictions of many among the accused. On February 6, 1481, six Conversos were found guilty of heresy and condemned to be burned at the stake. The Spanish Inquisition had begun after years of consideration, debate and negotiation.

As well as secret Jews, secret Muslims were also targeted (p. 152):

…the Spanish Inquisition is best remembered for its persecution of Conversos. But in addition, Muslims who had converted to Christianity were also investigated and for the same reasons. Those suspected of secretly practicing Islam after conversion were called Moriscos (meaning Moor-like), and the majority of these Moriscos resided in Granada, Aragon and Valencia. By law, all Muslims living in Castile were legally required to convert in 1502. Muslims in Aragon and Valencia were not legally required to convert until 1526, although the majority had undergone forced conversions during the Revolt of the Brotherhoods (1519–23).

Arguably, there was a measure of revenge in all this – retribution for the treatment of Catholics during the long years of Islamic domination. There was also the fear of a fifth column – Islam still dominated across the sea in North Africa, and the Ottoman empire was still expanding. However, it was lack of conformity to Catholicism that was the defining issue. Later, the Spanish Inquisition turned on the nascent Protestant movement (p. 169): ‘The Inquisition was most active against Protestants in the 1550s and 1560s. In 1558, inquisitors in Valladolid and Seville arrested many accused of practicing Lutheranism or sympathizing with the movement. Arrests included many members of the clergy and nobility.’ Their fates were no different than the Moriscos, even though they posed no military/political threat (p. 170):

On May 21, 1559, fourteen accused heretics were sentenced to death, including some already dead who were exhumed and their remains burned at the stake. In Seville on September 24 of the same year, more than one hundred more were condemned, with twenty-one receiving death penalties. In December 1560, seventeen more were burned at the stake. Most of the condemned in these trials were from the clergy and nobility. Their heresy was being Protestant, which inquisitors easily defined as a form of “error” or being knowingly heretical. An outcome of this sudden inquisitorial fervor against Lutherans was the beginning of anti–Inquisition expression. Pamphlets and books appeared around Europe protesting the punishments of Lutherans in Spain.


The Inquisition was a purely Roman Catholic institution, of which Protestants are innocent. Indeed, they were also its victims – and proto-Protestants like the Waldensians were among its earliest victims. The basic issue was heresy. However, as we have seen, Islamic Spain also punished heresy – along with blasphemy and apostasy. It follows that Muslim criticism of the Spanish Inquisition is a case of the pot calling the kettle black.