Nicodemus could not see how a grown man could start life over. He took Jesus' words about being "born again" in a physical sense. His first question asks how it is possible at all; his second pushes the idea to its impossible extreme. Barnes explains why the words puzzled him: Jewish teachers used "born again" for a Gentile becoming a Jew, "But they never used it as applicable to a Jew." So when Jesus said every man needs it, Nicodemus "supposed that there was an absurdity in the doctrine, or something that surpassed his comprehension." Matthew Henry says that what Christ spoke spiritually, Nicodemus "seems to have understood after a corporal and carnal manner."

Jesus answered by explaining what kind of birth He meant: "Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God" (John 3:5). "That which is born of the flesh is flesh; and that which is born of the Spirit is spirit" (John 3:6). He told Nicodemus not to marvel, and compared the Spirit's work to the wind, which "bloweth where it listeth" (John 3:7-8). Nicodemus still did not understand and asked, "How can these things be?" (John 3:9).

Nicodemus was no ordinary inquirer. Barnes says that as "a ruler of the Jews" he was "One of the Sanhedrin, or great council of the nation." He came "by night" (John 3:2); Barnes lists several possible reasons, including fear of "the ridicule and contempt of those in power," but adds that since no bad motive is imputed to him, and Jesus did not reprove him, charity should suppose his motives were good.

The Greek word translated "again" in John 3:3, 7 is anothen, which can mean "from above" or "anew, over again." Thayer's lexicon favors "anew" here, pointing out that Nicodemus wondered about being born a second time, not about being born from heaven. Both ideas fit Jesus' answer: a new birth that comes from the Spirit (John 3:5-6).

Nicodemus' question exposes the heart of the matter: no one can produce new life by human effort, any more than a man can be born a second time from his mother's womb. That is exactly Jesus' point. New birth is the work of the Spirit (John 3:6, 8). John had already written that God's children are born "not of blood, nor of the will of the flesh, nor of the will of man, but of God" (John 1:13).

Matthew Henry observes that "They that are proud of their first birth are hardly brought to a new birth." Nicodemus had every religious advantage, yet Jesus told him he needed what any Gentile needed. Henry also credits him: he "does not turn his back upon Christ because of his hard saying." Later, Nicodemus speaks up for Jesus before the council and helps bury Him (John 7:50-51; John 19:39).