The Spanish Inquisition is a popular topic among Skeptics who pair it with the Crusades as an example of how Christianity has ruined Western culture. Is this an overplayed issue, or a serious problem for the Christian faith?
The truth lies in between and is more a case of people being people rather than Christians being Christians. Our primary sources for this essay are the collected essays in The Inquisition edited by Brenda Stalcup and Henry Kamen's The Spanish Inquisition [K], an excellent myth-buster for this subject.
Where was the Inquisition?
Despite the common attribution, Spain was but one place where an Inquisition occurred, and the roots of it are actually in activities in France. It eventually spread all over Western Europe in a multitude of forms and for a multitude of purposes, then gradually died out, lasting at the latest until 1808 in Spain. It did not touch the British Isles, except briefly , or Scandinavia. Because the Spanish variation does get the most attention, we will keep a special focus on that and use Kamen's work as a guide.
Why was there an Inquisition?
Stalcup  asks the honest question, "How could the leaders of the church reconcile the terror and destruction wrought by the Inquisition with the doctrine of mercy taught by Christ?" The answer she gives is a familiar one -- one we have also seen given in answer to such questions as, "Why would a God of love order the Canaanites exterminated?" or "Why does Proverbs teach corporal punishment?"
Eventually, different forms of the Inquisition grew up in different places for different reasons, but in terms of why it started the simple answer is that the Inquisition was seen as an instrument of social survival.
Stalcup notes that the Catholic Church (CC) in the so-called Dark Ages "was the one stable institution that provided leadership and order" and quotes historian Bernard Hamilton as saying that "as the sole vehicle of a more civilized tradition in a barbarous world" the CC "became involved in social and political activities which formed no part of its essential mission, but which it alone was qualified to discharge." 
With the exception of a few Jews and Muslims, all people in Western Europe depended on the CC for meaning and survival. Any undermining of this social construct was a threat to the physical, mental, and spiritual well-being of the whole. Kamen likewise says of the Spanish variation, "It fulfilled a role...that no other institution fulfilled." [K82]
In this light, enter Catharism -- a heresy from the east that taught a spiritual dualism (which made Satan the creator of the material world, and in a reversal of Mormonism, argued that Satan made man, and that God pitied man and gave him a soul ), poverty, vegetarianism, honesty, and abstention.
Not a bad mix of principles at the end, but they also managed to accuse the CC of that day of abuses, to the point of calling the CC a tool of Satan  "designed to trick Christians into thinking that they had obtained salvation." The Cathars also refused to swear oaths of loyalty, "a stance that had the potential to undermine the authority of both the Catholic Church and the secular government."
By now the average Skeptic is saying, "Why didn't they just leave the Cathars alone"? If the Cathars had left things alone themselves, that may indeed have been the result, but their work was the moral equivalent in that day of not merely protest, but of laying bombs under the Capitol building.
As in OT cases we have no perception of how seriously Cathar actions undermined the social order and threatened to cut the links of the chain of survival, as well as (from that view) security in eternal life. The society of this time did not yet have the leisure to allow such powerful dissent and yet still be able to survive. The Inquisition's actions would be excessive today because we have the leisure to tolerate dissent with no threat to our survival -- not as yet, at any rate. As European society progressed, there indeed came to be less threat of heretics undermining corporate survival, so naturally the Inquisition process died out.
As time passed and as the Cathars disappeared, the Inquisition spread to other countries and acquired other targets, including, in Spain, Jews and Muslims who had professed to convert, but secretly had not (the former in some cases being denounced by other Jews -- K18 -- and being targeted not for religious reasons per se, but for social reasons -- K61). In Germany it targeted a sect called the Waldenses, and pantheists .
Beyond this point we will delve no further into the Inquisition's many manifestations outside of Spain, as it becomes complex enough to write entire books and it is enough to know that the roots of the Inquisition are not as simple as the Skeptics care to paint.
Whence the "inquiz" of the Inquisition?
Pope Innocent III did try to be moderate, at first, sending Cistercian monks to the region of France in 1198 where Catharism was getting a foothold. Their mission was to preach to the populace and identify the leaders of the heresy. Obviously, one had to "ask around" to find the leaders, hence the "inquis-" in the Inquisition, Part 1.
Catharism made the "inquis-" part a little hard, however. You would no doubt guess that the average peasant wasn't too keen on abstention, poverty, and vegetables, so most "believers" didn't take the official, saving rite to join Catharism, until they were on their deathbeds. Meanwhile, they still also participated in normal CC services.
This made it difficult to discern between almost all Cathars and non-Cathars, so that the movement was more insidious in its spread than it appeared, and it also gave the religious officials a tough moral choice, since they considered themselves to be responsible before God for the spiritual well-being of their flock , "answerable before God for the souls" of all in their charge.
Ironically enough it was the Cathars, not the CC, who struck the first mortal blow in 1208 when a local noble assassinated one of Innocent's special representatives. Innocent began the Albigensian Crusade and for 20 years scoured the land for Cathars. The common people, however, helped the leading Cathars escape or protected them, and at the same time, the Crusade evolved into a political battle over which Innocent lost control.
Thus a new tactic was developed -- the official "Inquisition" established in 1215. A similar act helped turn popular sentiment towards the Spanish Inquisition when Christianized Jews assassinated one of the Inquisitors in a cathedral, engendering a reaction one might compare to sentiment against Arabic peoples after the 9/11 bombing [K54].
What was the process?
The simple form was that Christians (or in Spain at one point, Jews) were required to "seek out heretics and deliver them to a special church tribunal for trial."  Those convicted would be excommunicated, then handed over to secular authorities for punishment, which was usually "banishment and the confiscation of their property."  Note well, not execution, but a punishment that would remove them from the social order they were threatening, though in Spain, execution by burning did become a normal sentence for the unrepentant.
Over the next 25 years the Inquisition worked in France, and followed a typical procedure  which was also roughly followed in Spain:
- One or more inquisitors arrived at a town or village and preached against the heresy.
- They offered a grace period of 7 to 30 days for heretics to recant and receive a "relatively light penance." At the same time citizens were ordered to turn in any known heretics, where refusal to comply would result in excommunication -- again, disconnection from the social order, an appropriate reply to one who would assist in undermining the social order upon which all lives depended.
As might be expected, some people abused this system and reported an unpopular neighbor, just to try and get rid of them. Kamen [K18, 176] notes examples of witnesses using the Inquisition to "pay off old scores". The Inquisitors, of course, didn't use modern legal safeguards, and did accept testimony from others uncritically  in a way that would make modern legal experts blanch, but that was the norm for jurisprudence even in secular realms of the day, and still is in some countries.
Kamen writes of the Spanish variation: "Judicially, the Inquisition was neither better nor worse than the secular courts," [K182] but did hurt itself in the publicity department by not making public its methods. Fear was the product not just of the authority figures, but of one's own neighbors: "The fear generated by the tribunal...usually had its origins in social disharmony." [K177] In this light, people reported all manner of odd things as "crimes" (i.e., in 1492 in Spain, "not knowing the creed, or eating meat in Lent, were taken as signs of Judaism" [K40]; later in the 1560s, eating meat on forbidden days was taken as a sign of Lutheranism [K98]) and testified to alleged offenses some 30 or even 50 years in the past [K62].
Blame Christianity? No, blame human nature.
- Blame also eons before the advent of a working legal system. After the grace period anyone suspected of heresy was brought before a tribunal and asked to confess. If the confession did not match what had been reported about them by others, they went to prison where they were advised to think it over. The same was done to those who protested their innocence.
Following this, various methods were used to gain a confession, including intense interrogations, pleas from family members, and at the extreme end, starvation and torture.
Blame Christianity? No, because this was the modus operandi for ancient legal systems as far back as Rome, differing only in specifics of application: "To some degree, the Inquisition's use of torture mirrored a trend in the secular judicial system. During the twelfth century, the courts of Europe started to revive the old Roman legal procedures, including the application of torture to extract confessions." [Emphasis added.] Some of this came from Justinian's code, which was in turn derived from earlier pagan law.
Moreover, the CC believed that the eternal soul's fate was of more importance than the body, which runs as a match to what we have observed elsewhere; namely, that the short-term destruction of peoples like the Amalekites and Canaanites are understandable in light of the long-term goals of social survival for people as a whole. To the Inquisitors, a few moments of pain on earth was a necessary price for saving someone from eternal torment.
Skeptics may claim that their priorities were wrong, but they can't fault them as much for their motives (though again, plenty of system abuses did take place).
- Once a confession was made, punishment ranged from fasting and prayer to a brief imprisonment. Those who had committed serious crimes were given life imprisonment (perhaps such as the one who assassinated Innocent's rep). Execution was reserved "for unrepentant or relapsed heretics"  under a view that heresy was a form of treason against eternal security.
The description given by Strayer and Munro sounds just right from any work by Malina and Rohrbaugh or Crenshaw on survival of society in the ANE or Greco-Roman world:
Heretics destroyed the bonds of society by weakening the basic authority on which all institutions rested; their mere existence brought down the vengeance of heaven on the regions in which they lived. Heresy was a disease which had to be wiped out; the heretic must either be cured or destroyed.
The regular reader will recognize that this very description could have described the Roman attitude towards Christianity as a superstition which broke down loyalty to the Roman gods who kept the world in order. This is not a Christian issue, but a social survival issue and a pattern followed by societies to preserve themselves -- until they reach our stage, where a fall is much harder to envision.
What About the Torture?
The shame of the Inquisition is the use of torture, and we need not explore the details, but here, human nature trumped and caused the worst of the problems. Torturers were only allowed to torture a prisoner once  but got around the rule by "suspending" a torture session until the next day to continue it.
On the other hand, compared to methods used by the secular penal system of the day -- which included being burned alive for counterfeiting and execution for thievery, and later being disemboweled or boiled to death -- the Inquisition wasn't as serious a threat to health and well-being as its secular counterparts. One of its more odious practices was posthumously denouncing persons, publicly burning their exhumed remains, and confiscating their property, leaving their family -- even if they were not heretics -- destitute. 
Imprisonment may well have been the most cruel of the Inquisition's penalties, as in all ancient jails, cells were cramped and unlit, so that at times prisoners could neither lie down nor stand. Only a "very tiny minority"  of persons withstood such treatment for months or even (up to 30) years without "confessing".  On the other hand, in the Spanish variation, the prisons of the Inquisition were generally -- not always -- better than those of the secular courts, so that, for example, a friar "made some heretical statements simply in order to be transferred from the prison he was in to that of the Inquisition." [K184])
It is worth noting that there are examples of the church officials wanting to be lenient, and mobs, fearing this leniency, breaking into a prison where Cathars were held and taking matters into their own hands, killing the Cathars themselves. Strayer identifies this as an example of the "feelings of fear and hatred among the mass of the people because [the Cathars] dissociated themselves completely from all the values on which society was based." 
For a parallel consider Sosthenes, the synagogue ruler, being beaten, and yes, Joseph Smith. However, where Catharism originally spread in France, the sympathies of the people were with the Cathars. This extreme of "solutions" by the people made it necessary for the church to take responsibility for instituting a uniform solution. The mixed response "was not a situation the Church could responsibly allow to continue." 
Kamen reports that the threat of the Spanish Inquisition has been particularly overblown. Without minimizing the atrocities that were committed, it is nevertheless a fact that many Skeptical sites (relying at times on Helen Ellerbee, a notoriously unreliable source) frame the Spanish Inquisition particularly as one might elsewhere frame Mao's Great Leap Forward. Kamen [K60, 203] notes that, "Taking into account all the tribunals of Spain up to about 1530, it is unlikely that more than two thousand people were executed for heresy by the Inquisition...for most of its existence that Inquisition was far from being a juggernaut of death either in intention or in capability."
By Kamen's estimate, for example, "it would seem that during the sixteenth and seventeenth centuries fewer than three people a year were executed in the whole of the Spanish monarchy from Sicily to Peru, certainly a lower rate than in any provincial court of justice in Spain or anywhere else in Europe." [K203] This was weighed against people of Jewish and Muslim origin, but let it never be said that the numbers themselves are anything to be especially outraged about. It is also notable that the impetus for the Inquisition in Spain came first not from the church, but from the king and queen of Spain who asked for an Inquisition to be conducted.
Statistically, over the life of the Spanish Inquisition, and in spite of spurts of major use, torture was "used infrequently" [K188] and only in cases of heresy [K189]. Despite possible claims of Skeptics, there was not enough sophistication in the Inquisitors to use torture for the purpose of brainwashing. "A comparison with the cruelty and mutilation common in secular tribunals shows the Inquisition in a relatively favourable light. This, in conjunction with the usually good level of prison conditions, makes it clear that the tribunal had little interest in cruelty and often attempted to temper justice with mercy." [K192]
One may as well credit Christianity for making the Inquisition less severe than it would have been had it been conducted by secular authorities addressing the same social fears and concerns. Prison sentences were often not literally observed. A "life sentence" could amount to only 10 years of incarceration [K201] and the term could be served at home, in a monastery, or in a hospital when prison space was limited. Kamen also notes that (despite Skeptical desires to see every Spaniard as cowering in fear awaiting a knock at the door from Torquemada himself) "over long periods of time and substantial areas of the country, [the Inquisition] quite simply did nothing." [! - K82] "In many Christian communities throughout Spain where internal discord was low and public solidarity high, fear of the Inquisition was virtually absent." A priest in Urgell, Spain, in 1632 said that "he didn't recognize the Inquisition and didn't give a fig for it" -- and the Inquisition was "unable to take any action against him, nor indeed was it able to impose its authority on the people of that diocese."
Resistance was not a matter of fighting off the Pope's armies, but of public cooperation: "Because the information available to inquisitors came not from their own investigations but almost exclusively from members of the public, it was in effect the public that dictated the forms of inquisitorial justice...where [ordinary people] refused to cooperate the tribunal was impotent and incapable of inspiring fear." [K178-9]
So, in conclusion: Blame Christianity for the Inquisition? Hardly. Blame human nature, yet again, which humanists are so proud of, and blame also a propaganda machine that was so effective that "even today it is difficult to separate fact from fiction." [K305]
Some reader observations based on a reading of this item:
The first is the link between the expulsion of the Moors from the Iberian peninsula and the Islamist threat to Christendom. Remember, the Islamist armies were only driven across the Danube out of eastern Europe in 1683, and in the period of the Inquisition, it seems plausible that Spain, among others, felt a heightened need to defend its self-identity.
There seems to be some overlap between Ferdinand and Isaballa and the last Islamic sultanate on the Iberian peninsula, the Nasrid Dynasty (1238-1492), which would place the commissioning of the Inquisition in a period of national civil war (Ever watched the Charlton Heston film, El Cid?).
The second is to note that, uncomfortable as it may seem, the Inquisition could not have lasted 400 years without popular support. Perhaps the people of Spain were motivated to look for the enemy within by their numerous enemies without.
The third is that any distinction between church and state may be somewhat artificial. If we read into the motives for the Inquisition a need to preserve social identity, we also need to see the Spanish people identifying themselves primarily with the church. The broad history of europe is that nation states emerged from Christendom, and in the 1400s it is possible that people saw their primary allegiance to God (through the church), followed by secondary allegiance to the civil authorities. One could debate the relative merits of such a world-view, but we should note that the major eruptions between the Roman Church and State in the following centuries came about, in part, because the Church saw the states as usurping its temporal power.
It is quite a different paradigm to the wall of separation that your founding fathers erected between Government and Religion, indeed their arrangement may have been an extreme reaction to the abuses observed in Europe. I know you have rebutted the skeptics for denouncing the Inquisition as a product of Christianity on this issue, but I think they should be given some credit for joining the dots to Spain's social, Christian, self-identity.
Finally, there's the question of whether the Inquisition was good or bad. This is the question behind your discussion on whether Christianity has had a good or bad influence on the world. It requires some philosophizing, in which we can do not much more than map out the extreme positions. One extreme is to take the existentialist view and say that these things happened, but we should not attach any value to them. The other is to moralize on the basis that the outcomes could have been better or worse had alternative strategies been taken.
The problems either way are that the existentialist cannot learn anything and that the moralizer has to reconcile himself to the fact that a greater good sometimes comes out of a great evil, and sometimes it happens the other way around. I also find it pertinent that no-one writes history (or reviews it) unless they have an agenda. It was true of the authors of the Biblical narratives, and it is true of every historian ever since.
I think that before we find ourselves shipwrecked on the sand-bars of relativism, we need to remind ourselves of the Christian position, which is that God will judge us all perfectly because only he has the perfect knowledge needed to make such a judgement.
Having said that, I would also say that Christianity has brought much benefit to the world. Its influence has been sorely under-rated by the Skeptics, which is perhaps your main point. To them I would suggest they get out more and travel to some parts where Christianity has not made a big impression.
Objection: You're rewriting history in regards to the Inquisitions. You minimalize its horrors and try to distance the Catholic Church from responsibility for it.
If that is what I am doing, then that is what is also being done by the professional historians I quoted. How did I (and they) "minimalize its horrors"? Did I report less of them than there actually were? Did Kamen under-report the death toll?
Torture is always bad and you can never justify it.
The answer is: I have a dilemma for you, and it's a real one that applies today. We have had dispute lately over whether it would be moral to torture Afghan prisoners in Cuba to get info on whether there were deadly terrorist attacks coming. So I'll put it this way. We have a prisoner named Ahmed who says he knows of an impending attack that will kill tens of thousands of people, but he refuses to offer the details. Do we use torture, or not?
The fact is that many intelligent people today find justification for torture when it serves a far greater good -- especially when it is a matter of evil individuals harming a larger number of innocents.
Are you saying that the Inquisition, at least in principle, is Biblically justified despite the occurrences during the Middle Ages?
No. Replace the word "Biblically" with "socially" and end the sentence at "justified".
I imagine, Hitler justified the short term destruction of the Jews because of his long-term goals (A thousand year Reich is a pretty long term).
He probably did, and he was in error precisely because his reasons were in error. Here's where the Skeptics have some analogy problems: The justification for torture in a hierarchy of morals lies only in a truly greater good -- as intended in my Ahmed example above. A false "greater good" -- as all but a few would agree with Hitler's case -- offers no justification.
So the questions return to, "Is it justified?" and the answer lies in, "Is there a greater good to be accomplished?" (i.e., saving tens of thousands from death) and at the same time, "Is the greater good for real?"
I think we ought to invite some Muslims to torture you to save you from the Hell reserved for people who believe in the Trinity. After all, who can fault my motives in this suggestion?
You can't, obviously, if Islam is true. That's the very point at issue.
The victims of the Inquisitors were not terrorists with plans to kill tens of thousands of people, but were simply people who were unlucky enough to be accused of heresy or witchcraft. Or they were Jews who would not convert. Or they had a lot of money that the inquistors wanted. Comparing the Inquisition's victims to terrorists is bogus.
Since Skeptics regard all religions as false, that is all the "victims" could be. But if religion is NOT false, then the "victims" were worse than terrorists -- they led people down a road to eternal punishment.
As for money, from what Kamen reported, the Spaniards at least made almost nothing, and what little they made went right back into funding their own efforts. Other property went to the local governments, not the church.
The Inquisitors are still morally at fault.
Let's answer that using that fanatical Muslim, who we called Ahmed. If he truly believes what he does, then by what information he has, he is doing the morally correct thing. He is only morally culpable IF he does not believe what he claims to believe.
Ahmed is, however, intellectually culpable because he believes something false. He pursues his moral code in ignorance, and is therefore not morally culpable for his actions. He is wrong, but does not know it.
By the same token, a police officer who shoots a man dead because he thought he saw a gun pulled is not morally culpable (unless he lies about it) if it is later found that what he thought was a gun was actually a cell phone.
Tie it in: The Inquisitors were not, as a whole, morally culpable for their actions if they understood there to be a real threat to society and to people's eternal fate.
In that light, Skeptics have no valid reason to accuse them of moral negligence. Skeptics can argue that the Inquisition was factually in error, based on other grounds, but in order for them to say that they were morally in error then they need to prove that the Inquizzers didn't actually believe they were helping people.