The concepts of an inquisition and inquisitorial procedure lie deep in the roots of european history. Inquisitions were used during the decline of the Roman Empire until the Spanish Inquisition's decline in the early 1800s. An inquisition can be run by both civil and church authorities in order to root out non-believers from a nation or religion. The Spanish Inquisition was one of the most deadly inquisitions in history.
The Spanish Inquisition was used for both political and religious reasons. Spain is a nation-state that was born out of religious struggle between numerous different belief systems including Catholicism, Islam, Protestantism and Judaism. Following the Crusades and the Reconquest of Spain by the Christian Spaniards the leaders of Spain needed a way to unify the country into a strong nation. Ferdinand and Isabella chose Catholicism to unite Spain and in 1478 asked permission of the pope to begin the Spanish Inquisition to purify the people of Spain. They began by driving out Jews, Protestants and other non-believers.
In 1483 Tomas de Torquemada became the inquisitor-general for most of Spain. He was responsible for establishing the rules of inquisitorial procedure and creating branches of the Inquisition in various cities. He remained the leader of the Spanish Inquisition for fifteen years and is believed to be responsible for the execution of around 2,000 Spaniards. The Catholic Church and the Pope attempted to intervene in the bloody Spanish Inquisition but were unable to wrench the extremely useful political tool from the hands of the Spanish rulers.
The Inquisition was run procedurally by the inquisitor-general who established local tribunals of the Inquisition. Accused heretics were identified by the general population and brought before the tribunal. The were given a chance to confess their heresy against the Catholic Church and were also encouraged to indict other heretics. If they admitted their wrongs and turned in other aggressors against the church they were either released or sentenced to a prison penalty. If they would not admit their heresy or indict others the accused were publicly introduced in a large ceremony before they were publicly killed or sentenced to a life in prison. Around the 1540s the Spanish Inquisition turned its fire on the Protestants in Spain in an attempt to further unify the nation. The Spanish Inquisition's reign of terror was finally suppressed in 1834.
In 1233, Pope Gregory IX pronounced the official beginning of "The Inquisition," and send a cadre of Dominican monks to carry it out. When they arrived in town, the Inquisitors laid out a deadline: Everyone had one month to confess all your warped, evil beliefs and come back into the fold, with only a minimal punishment.
When the month expired, all hell broke loose. The monks began staging trials, with the support of the local government. Any accusation of heresy was enough to start a trial going, and the names of the accusers were kept secret. The trials themselves were held in secret. After a brief flirtation with the concept of a "right to an attorney," all due process was dispensed with. The only appeal of a guilty verdict was to the pope.
Although you might have a picture of a quaint medieval hysteria, the Spanish Inquisition went on for THREE HUNDRED YEARS, lasting well into the 1800s. The first five years of the Spanish Inquisition were basically rampant mayhem with no appreciable diminishment of the "threat" from the fake Catholics. As a result, Tomas de Torquemada was appointed to whip the Inquisition into shape.
Thousands and thousands of "heretics" were burned at the stakes throughout the duration of the Spanish Inquisition (the exact numbers are unknown). There was no such thing as an "alleged" heretic under the Inquisitions reign of terror; there were only "repentant" and "unrepentant" heretics.
The Inquisitors came up with numerous gadgets to work within this restriction. They included:
The Judas Chair: This was a large pyramid-shaped "seat." Accused heretics were placed on top of it, with the point inserted into their anuses or genitalia, then very, very slowly lowered onto the point with ropes. The effect was to gradually stretch out the opening of choice in an extremely painful manner.
The Head Vice: Pretty straightforward concept. They put your head into a specially fitted vice, and tighten it until your teeth are crushed, your bones crack and eventually your eyes pop out of their sockets.
The Pear: A large bulbous gadget is inserted in the orifice of choice, whether mouth, anus or vagina. A lever on the device then causes it to slowly expand whilst inserted. Eventually points emerge from the tips. (Apparently, internal bleeding doesn't count as "breaking the skin.")
The Wheel: Heretics are strapped to a big wheel, and their bones are clubbed into shards.
Methods of execution
Sawing: Heretics were hung upside-down and sawed apart down the middle, starting at the crotch.
Disembowelment: Not the nice kind of disembowelment, where a samurai slits you wide open like a fish and you die in moments. A small hole is cut in the gut, then the intestines are drawn out slowly and carefully, keeping the victim alive for as much of the process as possible.
The Stake: Depending on how unrepentant a heretic might be, the process of burning at the stake could vary wildly. For instance, a fairly repentant heretic might be strangled, then burned. An entirely unrepentant heretic could be burned over the course of hours, using green wood or simply by placing them on top of hot coals and leaving them there.
The last burning organized by the Inquisition was in 1834, when the Spanish Inquisition was officially abolished. But though Torquemada's legacy has been laid to rest, the Inquisition lives on.
Based in Vatican City, the Holy Office of the Inquisition is still one of the most powerful branches of the Church hierarchy. In 1965, Pope Paul VI renamed the Inquisition as the Congregation of the Doctrine of the Faith, but it was still basically the Inquisition.

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