"It has been estimated that the victims of the Spanish Inquisition outnumber those of heathen Rome, and that more Protestants were executed by the Spaniards in a single reign, and in a single province of Holland, than Christians in the Roman empire during the first three centuries." (The History of the Church by Philip Schaff)
Even the New Advent Catholic Encyclopedia has a very lengthy entry on the Inquisition. While they try to justify it and minimize the numbers (as is to be expected) they had no choice but to document what went on with burnings at the stake and torture to elicit confessions, not to mention many other punishments which are not authorized by Christ:
...In the second half of the twelfth century, however, heresy in the form of Catharism* spread in truly alarming fashion, and not only menaced the Church's existence, but undermined the very foundations of Christian society. In opposition to this propaganda there grew up a kind of prescriptive law — at least throughout Germany, France, and Spain — which visited heresy with death by the flames... But one of the difficulties of the procedure is why torture was used as a means of learning the truth. On the one hand, the torture was continued until the accused confessed or intimated that he was willing to confess. On the other hand, it was not desired, as in fact it was not possible, to regard as freely made a confession wrung by torture... And the excesses of the Spanish Inquisition are largely due to the fact that in its administration civil purposes overshadowed the ecclesiastical...
*Note: While the Catholic Church calls Cathars heretics, they may actually have been "good" Christians opposed to Rome (just like the Reformers).