The purpose of the Gospel was, as we have seen, conceived and expressed in terms of a comparison and contrast with the other three Gospels. So it is no surprise to find more detailed questions of the relationship of St John's account to that of the other three evangelists constantly recurring in treatments of the Fourth Gospel. Differences between St John's Gospel and the Synoptics seem to have been recognised as a possible stumbling-block to faith from the very beginning. The Muratorian Canon appears to wish to reassure the believer on this score. Origen refers to some people, probably within the Church, who think that the discrepancies between the different Gospel records show that the evangelists are not absolutely reliable. One of the reasons given by the Alogoi for their rejection of the Fourth Gospel was the impossibility of squaring its chronology with that of the Synoptics, in particular the impossibility of finding a place in the Johannine record for the forty days in the wilderness.

The longer period of ministry required by the Johannine account was noticed by Irenaeus and put by him to positive use against the Valentinians. They had asserted a connection between the passion and the twelfth aeon, on the ground that Jesus suffered in the twelfth month after his baptism. Irenaeus objects by pointing out that, according to St John, Jesus visited Jerusalem for four distinct passovers, and that therefore the ministry must have extended over a much longer period than a single year.