Jesus asks how they could still miss His meaning. Having shown that bread was never a problem for Him, He says plainly that He "spake it not to you concerning bread" and repeats the warning. Gill explains that once bread is ruled out, Jesus "must be thought to speak figuratively and mystically." Barnes notes one reason the disciples stumbled: "the word leaven was not often used among the Jews to denote doctrines." So the question is both a gentle rebuke and a clear explanation.

The explanation worked. "Then understood they how that he bade them not beware of the leaven of bread, but of the doctrine of the Pharisees and of the Sadducees" (Matthew 16:12). Barnes says, "After this explanation, they immediately saw that he referred to their doctrines." Mark's account ends instead with Jesus' question, "How is it that ye do not understand?" (Mark 8:21), and there the warning names "the leaven of Herod" (Mark 8:15).

Barnes explains the picture: "Leaven is used in making bread." It "passes secretly, silently, but certainly," and he adds, "So it was with the doctrines of the Pharisees." Gill says that by the leaven of these groups "is meant their doctrine." The Pharisees and Sadducees, two religious parties among the Jewish leaders, had just come together to test Jesus by asking for "a sign from heaven" (Matthew 16:1). Jesus answered them, "O ye hypocrites, ye can discern the face of the sky; but can ye not discern the signs of the times?" (Matthew 16:3).

The disciples had to learn that Jesus' words often carry more than their surface meaning. Matthew Henry puts it this way: "Christ speaks of spiritual things under a similitude, and the disciples misunderstand him of carnal things." The warning came right after the religious leaders tested Him (Matthew 16:1-4). Jesus was guarding His disciples against teaching that could spread quietly through their thinking.

Here understanding comes through Jesus' patient explanation (Matthew 16:12). In the next scene, Peter confesses that Jesus is the Christ, and Jesus says, "flesh and blood hath not revealed it unto thee, but my Father which is in heaven" (Matthew 16:17). In both scenes understanding is given: here through Jesus' patient explanation, there by the Father's revealing.