Excerpt from the "Heresy" chapter of
Barbara G. Walker's
Man Made God

The great historian Henry Charles Lea considered the Inquisition "a standing mockery of justice—perhaps the most iniquitous that the arbitrary cruelty of man has ever devised.... Fanatic zeal, arbitrary cruelty and insatiable cupidity rivaled each other in building up a system unspeakably atrocious. It was a system which might well seem the invention of demons." 

Here's how it worked: 1. All procedures were kept secret. 2. "Common report" and hearsay were accepted as proof of guilt. 3. The accused was never told of the nature of the charges or allowed legal counsel. 4. Witnesses were kept concealed. 5. Perjurers, excommunicates or children could give evidence. 6. No favorable evidence or character witnesses were permitted. In any case, anyone who spoke for an accused heretic was arrested as an accomplice. 7. Torture was used always, without limit of duration or severity. (Official sources said that torture could be used "only once," but weeks or months of daily torturing were simply described as "continuations.") Even if the accused confessed before torture, the torture was applied anyway, to "validate" the confession. If the accused died under torture, the record stated that the devil broke his neck in prison. 8. The accused was forced to confirm under torture the names of "accomplices" suggested to him by the judges. 9. No accused person was found innocent....

In 1209, Pope Innocent II preached a great crusade against the Albigensians (also called Cathari), which resulted in the extermination of half the population of France. When the papal legate was asked how the crusaders might distinguish the heretics from the faithful, he answered: "Kill them all—God will know his own."  It has been written that more than a million people were slaughtered during this crusade.  Briffault says, "A people of rare gifts had been tortured, decimated, humiliated, despoiled... The precocious civilization which had promised to lead Europe in the path of culture was gone, and to Italy was transmitted the honour of the Renaissance." 

For more, see Man Made God.