Who was Jesus referring to when He said 'you are clean, but not all'?
Jesus was referring to Judas, the twelfth man, not to any part of Peter’s body. In John 13:10–11, after saying Peter was clean, He added “but not all,” because He knew who should betray Him and therefore said, “You are not all clean.”
Les explains that in John 13, Jesus is washing the disciples’ feet shortly before His crucifixion. When Peter asks for a full bath, Jesus tells him that one who is washed does not need another washing except to wash his feet, for he is clean every whit. Then Jesus says to Peter, “you are clean, but not all.” Les emphasizes that Jesus is not talking about part of Peter’s body; He is talking about the twelfth man, Judas. Verse 11 confirms this, for Jesus knew who should betray Him, therefore He said, “You are not all clean.”
Jesus saith to him, He that is washed needeth not save to wash his feet, but is clean every whit: and ye are clean, but not all.
For he knew who should betray him; therefore said he, Ye are not all clean.
More Questions
What did Jesus mean when He said 'he that is washed needeth not save to wash his feet'?
Jesus taught that a person who has already had a full bath does not need another bath, only to wash his feet — just as a priest who had bathed still needed to wash his feet and hands.