What does John 13:18 mean?

Earlier, Jesus referred to the difference between being "bathed" spiritually, to those who are spiritually "washed" (John 13:8–10). In context, the meaning is that salvation makes a person "clean," leaving only a need to maintain good fellowship with God through confession of sin (1 John 1:8–10). In that same statement, Jesus pointed out that not all of those present for the foot-washing were "clean." This was a reference to Judas, who has already begun the process of betraying Jesus to local religious leaders (Matthew 26:14–16).

Here Jesus refers to His prior comment about the happiness of obedience (John 13:17) by saying this does not apply to everyone present. In making this remark, Jesus also emphasizes that Judas' betrayal is not a surprise. Nor did Jesus make a mistake when adding Judas to the inner circle of twelve men. Jesus knew what He was doing and who He was choosing. That, in part, was meant to fulfill the prophetic statement of Psalm 41:9. An even deeper fulfillment of that prophecy will happen in the next moments, as Jesus literally shares food with Judas (John 13:26).