Even after Jesus explained, Nicodemus still could not grasp how the new birth could happen. He was no longer asking about a mother's womb (John 3:4); now he was asking how such a birth by the Spirit could happen. Barnes says "Nicodemus was still unwilling to admit the doctrine unless he understood it." Gill describes him as "Remaining still as ignorant as ever, though Christ had explained the phrase 'born again'." Matthew Henry writes that Christ's explanation, "it should seem, made it never the clearer to him." It is the honest question of a learned man who has reached the edge of what he can understand.

Jesus first answered with a question of His own: "Art thou a master of Israel, and knowest not these things?" (John 3:10). Then He spoke of His own testimony: "We speak that we do know, and testify that we have seen; and ye receive not our witness" (John 3:11). He pointed to the One who "came down from heaven" and said, "as Moses lifted up the serpent in the wilderness, even so must the Son of man be lifted up: That whosoever believeth in him should not perish, but have eternal life" (John 3:13-15).

Jesus' answer draws on a story from Israel's history. In Numbers 21:8-9, when the Israelites were bitten by serpents in the wilderness, Moses made "a serpent of brass, and put it upon a pole," and anyone bitten who looked at it lived. Jesus said He must be "lifted up" in the same way (John 3:14).

Jesus called Nicodemus "a master of Israel" (John 3:10), which the ESV renders "the teacher of Israel." Barnes notes Nicodemus was a member of the Sanhedrin, the great council of the nation, and says that as such a teacher "he ought to have understood this doctrine."

Nicodemus wanted to understand how before he would believe. Jesus' answer moved him from how to Who. The new birth is not explained by a formula; it comes through believing in the Son of man who would be lifted up (John 3:14-15).

Barnes observes that "people will often admit facts on other subjects, and be greatly perplexed by similar facts in religion." We accept the wind without seeing where it comes from (John 3:8). Matthew Henry's Concise Commentary adds, "Many think that cannot be proved, which they cannot believe." God does not ask us to understand everything before trusting Him, but to trust the One who knows and has come from heaven (John 3:13).