The term Inquisition comes from the Medieval Latin word "inquisitio", which referred to any court process that was based on Roman law, which had gradually come back into use during the late medieval period. Today, the English term "Inquisition" can apply to any one of several institutions that worked against heretics (or other offenders against canon law) within the judicial system of the Roman Catholic Church. Although the term Inquisition is usually applied to ecclesiastical courts of the Catholic Church, it has several different usages:

• an ecclesiastical tribunal,
• the institution of the Catholic Church for combating heresy,
• a number of historical expurgation movements against heresy (orchestrated by the Catholic Church or a Catholic state), or
• the trial of an individual accused of heresy.

The Inquisition, as a church-court, had no jurisdiction over Moors and Jews as such. Generally, the Inquisition was concerned only with the heretical behaviour of Catholic adherents or converts.

The overwhelming majority of sentences seem to have consisted of penances like wearing a cross sewn on one's clothes, going on pilgrimage, etc. When a suspect was convicted of unrepentant heresy, the inquisitorial tribunal was required by law to hand the person over to secular authorities for final sentencing, at which point a magistrate would determine the penalty, which was usually burning at the stake although the penalty varied based on local law. The laws were inclusive of proscriptions against certain religious crimes (heresy, etc.), and the punishments included death by burning, although usually the penalty was banishment or imprisonment for life, which was generally commuted after a few years. Thus the inquisitors generally knew what would be the fate of anyone so remanded.

The 1578 edition of the Directorium Inquisitorum (a standard Inquisitorial manual) spelled out the purpose of inquisitorial penalties: ... quoniam punitio non refertur primo & per se in correctionem & bonum eius qui punitur, sed in bonum publicum ut alij terreantur, & a malis committendis avocentur (translation: “... for punishment does not take place primarily and per se for the correction and good of the person punished, but for the public good in order that others may become terrified and weaned away from the evils they would commit”).

Before 1100, the Catholic Church suppressed what they believed to be heresy, usually through a system of ecclesiastical proscription or imprisonment, but without using torture, and seldom resorting to executions. Such punishments were opposed by a number of clergymen and theologians, although some countries punished heresy with the death penalty.

In the 12th century, to counter the spread of Catharism, prosecution of heretics became more frequent. The Church charged councils composed of bishops and archbishops with establishing inquisitions (the Episcopal Inquisition). The first Inquisition was temporarily established in Languedoc (south of France) in 1184. The murder of Pope Innocent's papal legate Pierre de Castelnau in 1208 sparked the Albigensian Crusade (1209-1229). The Inquisition was permanently established in 1229 (Council of Toulouse), run largely by the Dominicans in Rome and later at Carcassonne in Languedoc.

Historians use the term "Medieval Inquisition" to describe the various inquisitions that started around 1184, including the Episcopal Inquisition (1184-1230s) and later the Papal Inquisition (1230s). These inquisitions responded to large popular movements throughout Europe considered apostate or heretical to Christianity, in particular the Cathars in southern France and the Waldensians in both southern France and northern Italy. Other Inquisitions followed after these first inquisition movements. The legal basis for some inquisitorial activity came from Pope Innocent IV’s papal bull Ad extirpanda of 1252, which explicitly authorized (and defined the appropriate circumstances for) the use of torture by the Inquisition for eliciting confessions from heretics. However, Nicholas Eymerich, the inquisitor who wrote the "Directorium Inquisitorum", stated: 'Quaestiones sunt fallaces et ineficaces' ("interrogations via torture are misleading and futile"). By 1256 inquisitors were given absolution if they used instruments of torture.

In the 13th century, Pope Gregory IX (reigned 1227-1241) assigned the duty of carrying out inquisitions to the Dominican Order and Franciscan Order. By the end of the Middle Ages, England and Castile were the only large western nations without a papal inquisition. Most inquisitors were friars who taught theology and/or law in the universities. They used inquisitorial procedures, a common legal practice adapted from the earlier Ancient Roman court procedures. They judged heresy along with bishops and groups of "assessors" (clergy serving in a role that was roughly analogous to a jury or legal advisers), using the local authorities to establish a tribunal and to prosecute heretics. After 1200, a Grand Inquisitor headed each Inquisition. Grand Inquisitions persisted until the mid 19th century.

With the sharpening of debate and of conflict between the Protestant Reformation and the Catholic Counter-Reformation, Protestant societies came to see/use the Inquisition as a terrifying “Other,” while staunch Catholics regarded the Holy Office as a necessary bulwark against the spread of reprehensible heresies.

Witch-trials

While belief in witchcraft, and persecutions directed at or excused by it, were widespread in pre-Christian Europe, and reflected in Germanic law, the influence of the Church in the early medieval era resulted in the revocation of these laws in many places, bringing an end to traditional pagan witch hunts. Throughout the medieval era mainstream Christian teaching had denied the existence of witches and witchcraft, condemning it as pagan superstition. However, Christian influence on popular beliefs in witches and maleficium (harm committed by magic) failed to entirely eradicate folk belief in witches.

The fierce denunciation and persecution of supposed sorceresses that characterized the cruel witchhunts of a later age were not generally found in the first thirteen hundred years of the Christian era. The medieval Church distinguished between "white" and "black" magic. Local folk practice often mixed chants, incantations, and prayers to the appropriate patron saint to ward off storms, to protect cattle, or ensure a good harvest. Bonfires on Midsummer's Eve were intended to deflect natural catastrophes or the influence of fairies, ghosts, and witches. Plants, often harvested under particular conditions, were deemed effective in healing.

Black magic was that which was used for a malevolent purpose. This was generally dealt with through confession, repentance, and charitable work assigned as penance. Early Irish canons treated sorcery as a crime to be visited with excommunication until adequate penance had been performed. In 1258 Pope Alexander IV ruled that inquisitors should limit their involvement to those cases in which there was some clear presumption of heretical belief.

The prosecution of witchcraft generally became more prominent throughout the late medieval and Renaissance era, perhaps driven partly by the upheavals of the era – the Black Death, Hundred Years' War, and a gradual cooling of the climate that modern scientists call the Little Ice Age (between about the 15th and 19th centuries). Witches were sometimes blamed. Since the years of most intense witch-hunting largely coincide with the age of the Reformation, some historians point to the influence of the Reformation on the European witch-hunt.

Dominican priest Heinrich Kramer was assistant to the Archbishop of Salzburg. In 1484 Kramer requested that Pope Innocent VIII clarify his authority to prosecute witchcraft in Germany, where he had been refused assistance by the local ecclesiastical authorities. They maintained that Kramer could not legally function in their areas.

The papal bull Summis desiderantes affectibus sought to remedy this jurisdictional dispute by specifically identifying the dioceses of Mainz, Köln, Trier, Salzburg, and Bremen. Some scholars view the bull as "clearly political". The bull failed to ensure that Kramer obtained the support he had hoped for, in fact he was subsequently expelled from the city of Innsbruck by the local bishop, George Golzer, who ordered Kramer to stop making false accusations. Golzer described Kramer as senile in letters written shortly after the incident. This rebuke led Kramer to write a justification of his views on witchcraft in his book Malleus Maleficarum, written in 1486. In the book, Kramer stated his view that witchcraft was to blame for bad weather. The book is also noted for its animus against women. Despite Kramer's claim that the book gained acceptance from the clergy at the university of Cologne, it was in fact condemned by the clergy at Cologne for advocating views that violated Catholic doctrine and standard inquisitorial procedure. In 1538 the Spanish Inquisition cautioned its members not to believe everything the Malleus said.

Portugal and Spain in the late Middle Ages consisted largely of multicultural territories of Muslim and Jewish influence, reconquered from Islamic control, and the new Christian authorities could not assume that all their subjects would suddenly become and remain orthodox Roman Catholics. So the Inquisition in Iberia, in the lands of the Reconquista counties and kingdoms like León, Castile, and Aragon, had a special socio-political basis as well as more fundamental religious motives.

In some parts of Spain towards the end of the 14th century, there was a wave of violent anti-Judaism, encouraged by the preaching of Ferrand Martinez, Archdeacon of Écija. In the pogroms of June 1391 in Seville, hundreds of Jews were killed, and the synagogue was completely destroyed. The number of people killed was also high in other cities, such as Córdoba, Valencia, and Barcelona.

One of the consequences of these pogroms was the mass conversion of thousands of surviving Jews. Forced baptism was contrary to the law of the Catholic Church, and theoretically anybody who had been forcibly baptized could legally return to Judaism. However, this was very narrowly interpreted. Legal definitions of the time theoretically acknowledged that a forced baptism was not a valid sacrament, but confined this to cases where it was literally administered by physical force. A person who had consented to baptism under threat of death or serious injury was still regarded as a voluntary convert, and accordingly forbidden to revert to Judaism.[38] After the public violence, many of the converted "felt it safer to remain in their new religion". Thus, after 1391, a new social group appeared and were referred to as conversos or New Christians.

King Ferdinand II of Aragon and Queen Isabella I of Castile established the Spanish Inquisition in 1478. In contrast to the previous inquisitions, it operated completely under royal Christian authority, though staffed by clergy and orders, and independently of the Holy See. It operated in Spain and in all Spanish colonies and territories, which included the Canary Islands, the Kingdom of Naples, and all Spanish possessions in North, Central, and South America. It primarily focused upon forced converts from Islam (Moriscos, Conversos and secret Moors) and from Judaism (Conversos, Crypto-Jews and Marranos) — both groups still resided in Spain after the end of the Islamic control of Spain — who came under suspicion of either continuing to adhere to their old religion or of having fallen back into it.

In 1492 all Jews who had not converted were expelled from Spain; those who converted became nominal Catholics and thus subject to the Inquisition.

Inquisition in the Spanish overseas empire

In the Americas, King Philip II set up three tribunals (each formally titled Tribunal del Santo Oficio de la Inquisición) in 1569, one in Mexico, Cartagena de Indias (in modern-day Colombia) and Peru. The Mexican office administered Mexico (central and southeastern Mexico), Nueva Galicia (northern and western Mexico), the Audiencias of Guatemala (Guatemala, Chiapas, El Salvador, Honduras, Nicaragua, Costa Rica), and the Spanish East Indies. The Peruvian Inquisition, based in Lima, administered all the Spanish territories in South America and Panama.

The wars of independence of the former Spanish colonies in the Americas concluded with the abolition of the Inquisition in every quarter of Hispanic America between 1813 and 1825.

By decree of Napoleon's government in 1797, the Inquisition in Venice was abolished in 1806.

In Portugal, in the wake of the Liberal Revolution of 1820, the "General Extraordinary and Constituent Courts of the Portuguese Nation" abolished the Portuguese inquisition in 1821.

The last execution of the Inquisition was in Spain in 1826. This was the execution by garroting of the school teacher Cayetano Ripoll for purportedly teaching Deism in his school. In Spain the practices of the Inquisition were finally outlawed in 1834.

In Italy, after the restoration of the Pope as the ruler of the Papal States in 1814, the activity of the Papal States Inquisition continued on until the mid-19th century, notably in the well-publicised Mortara affair (1858-1870). In 1908 the name of the Congregation became "The Sacred Congregation of the Holy Office", which in 1965 further changed to "Congregation for the Doctrine of the Faith", as retained to the present day.

Beginning in the 19th century, historians have gradually compiled statistics drawn from the surviving court records, from which estimates have been calculated by adjusting the recorded number of convictions by the average rate of document loss for each time period. Gustav Henningsen and Jaime Contreras studied the records of the Spanish Inquisition, which list 44,674 cases of which 826 resulted in executions in person and 778 in effigy (i.e. a straw dummy was burned in place of the person). William Monter estimated there were 1000 executions between 1530-1630 and 250 between 1630-1730. Jean-Pierre Dedieu studied the records of Toledo's tribunal, which put 12,000 people on trial. For the period prior to 1530, Henry Kamen estimated there were about 2,000 executions in all of Spain’s tribunals. Italian Renaissance history professor and Inquisition expert Carlo Ginzburg had his doubts about using statistics to reach a judgment about the period. "In many cases, we don’t have the evidence, the evidence has been lost," said Ginzburg.