Therefore while we are unwilling simply to concede the name of Church to the Papists we do not deny that there are churches among them. The question we raise only relates to the true and legitimate constitution of the Church, implying communion in sacred rites, which are the signs of profession, and especially in doctrine. Daniel and Paul foretold that Antichrist would sit in the temple of God, (Dan. 9: 27; 2Th 2: 4); we regard the Roman Pontiff as the leader and standard-bearer of that wicked and abominable kingdom.
By placing his seat in the temple of God, it is intimated that his kingdom would not be such as to destroy the name either of Christ or of his Church. Hence, then, it is obvious, that we do not at all deny that churches remain under his tyranny; churches, however, which by sacrilegious impiety he has profaned, by cruel domination has oppressed, by evil and deadly doctrines like poisoned potions has corrupted and almost slain; churches where Christ lies half-buried, the gospel is suppressed, piety is put to flight, and the worship of God almost abolished; where, in short, all things are in such disorder as to present the appearance of Babylon rather than the holy city of God.
In one word, I call them churches, inasmuch as the Lord there wondrously preserves some remains of his people, though miserably torn and scattered, and inasmuch as some symbols of the Church still remain – symbols especially whose efficacy neither the craft of the devil nor human depravity can destroy. But as, on the other hand, those marks to which we ought especially to have respect in this discussion are effaced, I say that the whole body, as well as every single assembly, want the form of a legitimate Church. (Institutes of the Christian Religion, Book Four, Chapter 2, 698)