But is it really true that apocryphal gospels were as popular and widespread as the canonical Gospels? Were they really on equal footing? Three pieces of evidence suggest otherwise.
Extant manuscripts. The physical remains of writings can give us an indication of their relative popularity. Such remains can tell us which books were used, read, and copied. When we examine the physical remains of Christian texts from the earliest centuries (second and third), we quickly discover that the New Testament writings were far and away the most popular. Currently we have more than 60 extant manuscripts (in whole or in part) of the New Testament from this time period, with most of our copies coming from Matthew, John, Luke, Acts, Romans, Hebrews, and Revelation. The Gospel of John proves to be the most popular of all with 18 manuscripts, a number of which derive from the second century (e.g., P52, P90, P66, P75). Matthew is not far behind with 12 manuscripts; and some of these also have been dated to the second century (e.g., P64-67, P77, P103, P104).
During the same time period, the second and third centuries, we possess approximately 17 manuscripts of apocryphal writings such as the Gospel of Thomas, the Gospel of Mary, the Gospel of Peter, the Protevangelium of James, and more. The Gospel of Thomas has the most manuscripts of all, with just three.
The implications of this numerical disparity have not been missed by modern scholars. Larry Hurtado argues that the low numbers of apocryphal manuscripts "do not justify any notion that these writings were particularly favored" and that whatever circles used these writings "were likely a clear minority among Christians of the second and third centuries."  Similarly, C. H. Roberts observes, "Once the evidence of the papyri is available, indisputably Gnostic texts are conspicuous by their rarity."  Scott Charlesworth agrees: "If the 'heterodox' were in the majority for so long, the non-canonical gospels should have been preserved in greater numbers in Egypt." 
Frequency of citation. While scholars typically focus on whether apocryphal books are cited, they have not paid sufficient attention to how often they are cited in comparison to the canonical writings. When those data are considered, the disparity between apocryphal and canonical writings becomes even more evident.
Take, for example, Clement of Alexandria, often mentioned as an early church father who prefers canonical and apocryphal writings equally. However, when the frequency of citations is considered, this claim proves to be unfounded—Clement vastly prefers the New Testament books to the apocryphal literature or other Christian writings. J. A. Brooks has observed that Clement cites the canonical books "about 16 times more often than apocryphal and patristic writings."  This disparity is thrown into sharper relief when we consider just the four Gospels. According to the work of Bernard Mutschler, Clement references Matthew 757 times, Luke 402 times, John 331 times, and Mark 182 times.  Comparatively, Clement cites apocryphal gospels only 16 times.  Apparently, Clement was not in doubt about which books he regarded as canonical.
Manner of citation. If indeed apocryphal writings were valued equally with canonical writings, we would expect such a fact to be reflected in the way these books are cited. Do the early church fathers cite apocryphal writings as Scripture? Rarely. In a few instances, it seems that books like the Shepherd of Hermas or the Epistle of Barnabas were regarded as having a scriptural status. But this was a small minority view. When we examine which books early Christians were not simply using but books they actually regarded as Scripture, then the canonical books are far and away the most popular. This is confirmed by the fact that there was a "core" canon of books in place by the middle of the second century.
Additionally, a number of these apocryphal writings were expressly condemned by the earliest Christians. Take, for example, the oft-discussed Gospel of Thomas. This book is never mentioned in any early canonical list, not found in any of our New Testament manuscript collections, never figured prominently in canonical discussions, and often was condemned outright by a variety of church fathers.  Thus, if Thomas was a widely read and widely received account, then it has left little historical evidence of that fact.
Everybody loves a good conspiracy theory. It would certainly be far more entertaining if someone could show that apocryphal books were really the Scripture of the early church and that they have been suppressed by the political machinations of the later church (i.e., Constantine). But the truth is far less sensational. While apocryphal books were given some scriptural status from time to time, the overwhelming majority of early Christians preferred the books that are now in our New Testament canon. Thus, we are reminded again that the church did not arbitrarily "create" the canon in the fourth or fifth century. Rather the affirmations of the later church simply reflected what had already been the case for many, many years.
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 H. Koester, "Apocryphal and Canonical Gospels," Harvard Theological Review 73 (1980): 106.
 Koester, "Apocryphal and Canonical Gospels," 107.
 W. L. Petersen, "The Diatesseron and the Fourfold Gospel," in The Earliest Gospels (ed. C. Horton; London and New York: T&T Clark International, 2004), 51.
 Larry Hurtado, The Earliest Christian Artifacts, 21-22.
 C. H. Roberts, Manuscript, Society and Belief, 52.
 Scott Charlesworth, "Indicators of "Catholicity" in Early Gospel Manuscripts," in The Early Text of the New Testament (ed. C. E. Hill and M. J. Kruger; Oxford: Oxford University Press, 2013).
 J. A. Brooks, "Clement of Alexandria," 48.
 Bernard Mutschler, Irenäus als johanneischer Theologe (Tübingen: Mohr Siebeck, 2004), 101.
 Brooks, "Clement of Alexandria," 44.
 E.g., Hippolytus, Ref. 5.7.20; Origen, Hom. Luc. 1; Eusebius, Hist. eccl. 3.25.6.
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Michael J. Kruger will participate in one of two dinner panels hosted by our The Gospel Coalition 2013 National Conference's Premier Sponsor, Reformed Theological Seminary, next month in Orlando. The topic of the panel will be "Having Confidence in the Scriptures." Kruger—from RTS Charlotte—will be joined on the panel by John Currid, Bruce Baugus, Chuck Hill, and Justin Taylor (moderator). Here is a brief description of what you can expect on Monday, April 8, at 5:30 p.m.:
Even as they affirm the inspiration, inerrancy, and infallibility of God's Word, Christians sometimes struggle to have confidence in the Scriptures. The Bible is attacked from outside the church and often minimized within the church. This panel will strengthen our confidence in the truthfulness and trustworthiness of the Scriptures, both Old and New Testaments.