The Bible itself records instances where God commanded that formal, legal inquiries—that is, inquisitions—be carried out to expose secret believers in false religions. In Deuteronomy 17:2–5 God said: "If there is found among you, within any of your towns which the Lord your God gives you, a man or woman who does what is evil in the sight of the Lord your God, in transgressing his covenant, and has gone and served other gods and worshiped them, or the sun or the moon or any of the host of heaven, which I have forbidden, and it is told you and you hear of it; then you shall inquire diligently [note that phrase: "inquire diligently"], and if it is true and certain that such an abominable thing has been done in Israel, then you shall bring forth to your gates that man or woman who has done this evil thing, and you shall stone that man or woman to death with stones."<quoted text>Is it your words or your deeds that identifies one as a christian? Can one live like the devil if they say they are christians and really be taken seriously?
It is clear that there were some Israelites who posed as believers in and keepers of the covenant with Yahweh, while inwardly they did not believe and secretly practiced false religions, and even tried to spread them (cf. Deut. 13:6–11). To protect the kingdom from such hidden heresy, these secret practitioners of false religions had to be rooted out and expelled from the community. This directive from the Lord applied even to whole cities that turned away from the true religion (Deut. 13:12–18). Like Israel, medieval Europe was a society of Christian kingdoms that were formally consecrated to the Lord Jesus Christ. It is therefore quite understandable that these Catholics would read their Bibles and conclude that for the good of their Christian society they, like the Israelites before them, "must purge the evil from the midst of you" (Deut. 13:5, 17:7, 12). Paul repeats this principle in 1 Corinthians 5:13.
These same texts were interpreted similarly by the first Protestants, who also tried to root out and punish those they regarded as heretics. Luther and Calvin both endorsed the right of the state to protect society by purging false religion. In fact, Calvin not only banished from Geneva those who did not share his views, he permitted and in some cases ordered others to be executed for "heresy" (e.g. Jacques Gouet, tortured and beheaded in 1547; and Michael Servetus, burned at the stake in 1553). In England and Ireland, Reformers engaged in their own ruthless inquisitions and executions. Conservative estimates indicate that thousands of English and Irish Catholics were put to death—many by being hanged, drawn, and quartered—for practicing the Catholic faith and refusing to become Protestant. An even greater number were forced to flee to the Continent for their safety. We point this out to show that the situation was a two-way street; and both sides easily understood the Bible to require the use of penal sanctions to root out false religion from Christian society.
The fact that the Protestant Reformers also created inquisitions to root out Catholics and others who did not fall into line with the doctrines of the local Protestant sect shows that the existence of an inquisition does not prove that a movement is not of God. Protestants cannot make this claim against Catholics without having it backfire on themselves. Neither can Catholics make such a charge against Protestants. The truth of a particular system of belief must be decided on other grounds.