Origin of the Reformed "Marks of the True Church"

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Calvin dedicates an entire Book of his Institutes (Book IV) to the Church, and Chapters 1-2 are about the "true church" in which he mentions the marks of a true church.

From 4.1.9:

Wherever we see the word of God sincerely preached and heard, wherever we see the sacraments administered according to the institution of Christ, there we cannot have any doubt that the church of God has some existence, since his promise cannot fail,

"Where two or three are gathered together in my name, there am I in the midst of them" (Matthew 18:20)

So here he lays out the first two points you mention - preaching and sacraments, but while he talks about discipline at length in 4.12 & 4.13, he doesn't include it in his "marks" in 4.1 and 4.2.

Since Calvin's Institutes were published in 1536, before the letter he mentioned, I suspect he had only recently begun to develop the marks in his mind. By the time he wrote the letter in 1539, he'd added the third mark.

However, I dug a little deeper and while browsing The Apostolic Fathers , a collection of letters and sermons by early church fathers, I found a document entitled The Didache, or The Teaching of the Twelve Apostles. This is likely a composite document, pieced together by early church fathers, and the author is unknown, but it dates somewhere from A.D 50 to 300, so it's well before Calvin (and Augustine, assuming he had anything to say about it)

In Didache are three "marks" (though not declared as distinguishing points; they are given as instructions) of a church (emphasis mine):

On the Lord's own day gather together and break bread and give thanks, having first confessed your sins so that your sacrifice may be pure. But let no one who has a quarrel with a companion join you until they have been reconciled, so that your sacrifice may not be defiled. For this is the sacrifice concerning which the Lord said, "In every place and time offer me a pure sacrifice, for I am a great king, says the Lord, and my name is marvelous among the nations" (Mal. 1:11, 14)

Therefore appoint for yourselves bishops and deacons worthy of the Lord, men who are humble and not avaricious and true and approved, for they too carry out for you the ministry of the prophets and teachers. You must not, therefore, despise them, for they are your honored men, along with the prophets and teachers.

Furthermore, correct one another, not in anger but in peace, as you find in the Gospel; and if anyone wrongs his neighbor, let no one speak to him, nor let him hear a word from you, until he repents

The first paragraph, given the stipulation to repent sins before the sacrifice, seems to be talking about the Lord's Supper: sacraments.

The second paragraph speaks of establishing teachers: preaching the word.

The third paragraph gives instructions for how to treat a non-repentant sinner: discipline

Though it doesn't label them marks in so many words, I think this is the closest (and earliest) you'll find to the idea of the three distinguishing factors. I'm fairly certain, however, that Calvin was the one who called them "marks" first.

Ultimately, I think the general idea stems from Acts 2:42

And they devoted themselves to the apostles' teaching and fellowship, to the breaking of bread and the prayers.

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