Who was Jesus referring to when he said 'you are not all clean'?
He was referring to Judas, called the twelfth man, who would betray Him. Scripture explains that Jesus knew who should betray Him, so when He said 'you are not all clean' after washing the disciples' feet, He was not speaking about part of Peter's body but about Judas's uncleanness.
Les explains that in John 13, when Jesus washed the disciples' feet, Peter thought a fuller washing was needed, saying, 'Lord, then not my feet only, but also my hands and my feet.' Jesus answered that one who is washed is clean every whit, except for the feet, and said to Peter, 'you are clean, but not all.' Les clarifies that Jesus was not talking about part of Peter's body; He was 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.