The Gospel of John: The Word Became Flesh

John 3

John 3 — Born from Above by the Son Who Was Lifted Up

Today’s Passage: John 3

A leading Pharisee comes to Jesus under cover of night, and almost before the pleasantries are finished the conversation turns: you must be born again. From that collision the whole chapter rises, moving from a birth that only God can give, to a Son lifted up like the bronze serpent in the wilderness, to the single sentence the church has committed to memory above all others. And it closes gently, with John the Baptist stepping back so that Christ can fill the frame, content to say, “He must increase; I must decrease.” One spine runs the whole way through, and it is this: the new birth comes to us by looking, in faith, at the Son who was lifted up.

As you read, hold this: Born from above by the Son who was lifted up.

Context The world of John 3

Nicodemus is introduced with three marks of standing, each one weightier than the last. He is of the Pharisees, he is a leader of the Jews, and Jesus Himself calls him “Israel’s teacher.” He is almost certainly a member of the Sanhedrin, the very best of the establishment, and here he is coming to a young Galilean rabbi. He comes at night, and John, who makes light and darkness one of the master themes of his Gospel, means for us to notice it. Here is a man still standing in the dark, drawn toward the Light but not yet willing to be seen in it. It is worth watching his arc across the whole book, for he will speak up cautiously on Jesus’ behalf in 7:50–51, and in the end he will help bury Him in broad daylight, bringing a king’s weight of spices to the tomb (19:39).

Talk of being born again was not entirely foreign to his ears, for a Gentile who converted to Judaism was sometimes spoken of as a newborn child. What startles is that Jesus aims the language at Nicodemus himself, the consummate insider. Israel’s own teacher, a son of Abraham and a lifelong keeper of the Law, is told that he too must be born all over again from above. Pedigree counts for nothing here, and no weight of religious credentials will serve, because the kingdom is entered only by a birth that God alone can give.

When Jesus reaches for an image of His own death, He chooses one that Nicodemus would know by heart. In the wilderness, venomous snakes were killing the rebellious Israelites, and God told Moses to mount a bronze serpent on a pole, so that whoever had been bitten needed only to look at it and live (Numbers 21:8–9). Jesus says that the Son of Man must be “lifted up” in just the same way, and in John’s Gospel that single verb means crucifixion and exaltation at once. The cross is the pole, and the dying need only look to it in faith and live.

The second half of the chapter returns to John the Baptist, whose disciples have grown anxious that Jesus is now drawing the bigger crowds. John’s answer to them is one of the noblest sentences in all of Scripture, for he casts himself simply as the friend of the bridegroom, the best man whose whole joy is to hear the groom’s voice and then gladly step aside.

John 3:1–8 (BSB)

¹ Now there was a man of the Pharisees named Nicodemus, a leader of the Jews. ² He came to Jesus at night and said, “Rabbi, we know that You are a teacher who has come from God. For no one could perform the signs You are doing if God were not with him.” ³ Jesus replied, “Truly, truly, I tell you, no one can see the kingdom of God unless he is born again.” ⁴ “How can a man be born when he is old?” Nicodemus asked. “Can he enter his mother’s womb a second time to be born?” ⁵ Jesus answered, “Truly, truly, I tell you, no one can enter the kingdom of God unless he is born of water and the Spirit. ⁶ Flesh is born of flesh, but spirit is born of the Spirit. ⁷ Do not be amazed that I said, ‘You must be born again.’ ⁸ The wind blows where it wishes. You hear its sound, but you do not know where it comes from or where it is going. So it is with everyone born of the Spirit.”

Nicodemus opens with a careful, respectful compliment, and Jesus does not even pause to acknowledge it, answering instead a question that has not yet been asked. You cannot so much as see the kingdom, He says, unless you are born anōthen, pronounced AH-no-then. Strong's G509, from above; again, anew. This is the very hinge of the conversation, and it cannot be carried into English without losing something along the way. Anōthen means both “again, anew” and “from above,” and it is built from the little word anō, which means above. So when Jesus says a man must be born anōthen, He means born from above, born of God, born from heaven. Nicodemus, however, catches only the other sense, again, and so he stumbles straight into the absurd, wondering aloud whether a grown man can enter his mother’s womb a second time. That misunderstanding is precisely the point, for he is straining to fit a heavenly reality into an earthly category. The new birth is not the first birth repeated; it is a birth from above, and God alone can give it. The same word returns near the end of the Gospel, in 19:11, where Jesus tells Pilate that his authority has been given to him from above. . That doubled “Truly, truly,” which in the Greek is amēn amēn, is John’s own signal that something solemn is about to be said. Jesus will not be received as merely a remarkable teacher, for to meet Him at all a person must be remade from the inside out.

Nicodemus hears the word “again” and lands, predictably, back in the womb, and Jesus gently lifts him higher. To be born of water and the Spirit almost surely points to the cleansing and the new Spirit that Ezekiel 36 had promised long before. Flesh is born of flesh and spirit is born of the Spirit; these are two entirely different orders, and the first birth simply cannot produce the second. Then comes the image, built on the word pneuma, which means Spirit and wind and breath all at once. The wind blows wherever it wishes, and you hear the sound of it, yet you can neither command it nor chart its course. So it is with the Spirit’s birthing work, which is sovereign, free, unmistakable in its effects, and hidden in its source. You no more arrange your own new birth than you schedule the wind.

John 3:9–15 (BSB)

⁹ “How can this be?” Nicodemus asked. ¹⁰ “You are Israel’s teacher,” said Jesus, “and you do not understand these things? ¹¹ Truly, truly, I tell you, we speak of what we know, and we testify to what we have seen, and yet you people do not accept our testimony. ¹² If I have told you about earthly things and you do not believe, how will you believe if I tell you about heavenly things? ¹³ No one has ascended into heaven except the One who descended from heaven—the Son of Man. ¹⁴ Just as Moses lifted up the snake in the wilderness, so the Son of Man must be lifted up, ¹⁵ that everyone who believes in Him may have eternal life.

His “How can this be?” draws a gentle rebuke, for the master teacher of Israel, of all people, should have recognized the new heart that his own Scriptures had promised. Then verse 13 makes a staggering claim, and makes it quietly. No human being has ever climbed up to heaven to bring its secrets back down, and the only reliable witness to heavenly things is the One who first came down from them, the Son of Man now standing in front of Nicodemus. In a single sentence the whole human project of climbing up to God is turned on its head. We did not ascend to Him; God came down.

Then the conversation turns toward the cross, and the bronze serpent becomes the pattern. Those who were dying in the wilderness were healed not by doing anything at all, but simply by looking at what had been lifted up on the pole. “Lifted up” carries a double horizon here, for it means both raised upon a cross and raised into glory, since for John the crucifixion is itself the exaltation. Salvation comes to us the very way healing came to Israel, not by climbing but by looking in faith to the One who was lifted up for our sake. This is Article 5 of our faith set inside a wilderness image: the Son, standing as our substitute, lifted up so that everyone who believes in Him may have life.

John 3:16–21 (BSB)

¹⁶ For God so loved the world that He gave His one and only Son, that everyone who believes in Him shall not perish but have eternal life. ¹⁷ For God did not send His Son into the world to condemn the world, but to save the world through Him. ¹⁸ Whoever believes in Him is not condemned, but whoever does not believe has already been condemned, because he has not believed in the name of God’s one and only Son. ¹⁹ And this is the verdict: The Light has come into the world, but men loved the darkness rather than the Light because their deeds were evil. ²⁰ Everyone who does evil hates the Light, and does not come into the Light for fear that his deeds will be exposed. ²¹ But whoever practices the truth comes into the Light, so that it may be seen clearly that what he has done has been accomplished in God.

The most beloved sentence in all of Scripture earns its place here by sitting squarely on the spine we have been walking all along. We are born from above, but how? God loved the world in this way: He gave His one and only Son. And the world He loved is no pristine creation, but the world of verse 19, the world that loved the darkness, so that His love falls upon the alienated and the hostile. He gave the Son, not a servant and not an angel, but the only Son of His own kind, so that everyone who believes should not perish but have eternal life. That is the whole sentence, and it is best not broken apart into a stack of slogans. Let it stand as it is and do its work.

Verse 17 then fences the truth about God’s own heart, for His posture in sending the Son is rescue and not prosecution. Verse 18 lays the two destinies side by side. The one who believes is not condemned, while the one who refuses to believe is condemned already, not by some future verdict but by his present refusal of the only Son. Condemnation is not a new project God takes up against the world; it is the existing diagnosis that the Son came down to cure.

Why would anyone refuse such a love as this? John’s answer is uncomfortable and perfectly clear: unbelief is finally a matter of the heart’s loves and not the mind’s honest doubts. Men loved the darkness, and the evildoer avoids the Light the way a thief avoids a streetlamp, for fear that his deeds will be exposed. The one who does the truth, by contrast, comes gladly into the Light, content to have his whole life seen as the work of God. Which way a person turns when the Light arrives reveals everything about him. And we remember that Nicodemus came at night, so that the chapter is quietly asking, all the way through, whether he will yet step out into the day.

John 3:22–30 (BSB)

²² After this, Jesus and His disciples went into the Judean countryside, where He spent some time with them and baptized. ²³ Now John was also baptizing at Aenon near Salim, because the water was plentiful there, and people kept coming to be baptized. ²⁴ (For John had not yet been thrown into prison.) ²⁵ Then a dispute arose between John’s disciples and a certain Jew over the issue of ceremonial washing. ²⁶ So John’s disciples came to him and said, “Look, Rabbi, the One who was with you beyond the Jordan, the One you testified about—He is baptizing, and everyone is going to Him.” ²⁷ John replied, “A man can receive only what is given him from heaven. ²⁸ You yourselves can testify that I said, ‘I am not the Christ, but am sent ahead of Him.’ ²⁹ The bride belongs to the bridegroom. The friend of the bridegroom stands and listens for him, and is overjoyed to hear the bridegroom’s voice. That joy is mine, and it is now complete. ³⁰ He must increase; I must decrease.

The scene now shifts from a private conversation in the night to the open air of the river, where two baptisms are running at once. John’s disciples are wounded on his behalf, troubled that everyone is going to Jesus, but John’s reply is a humility that turns out to be pure joy. A man can receive only what is given to him from heaven, he tells them, and then he reaches for a wedding. He is not the groom; he is only the groom’s friend, and the best man’s whole happiness lies in hearing the bridegroom’s voice and watching the wedding go forward. “That joy is mine, and it is now complete.” And then the very summit of the scene: “He must increase; I must decrease.” This is not the sound of defeat but the deliberate, glad self-effacement of a man who knows exactly who he is and exactly who Jesus is.

John 3:31–36 (BSB)

³¹ The One who comes from above is above all. The one who is from the earth belongs to the earth and speaks as one from the earth. The One who comes from heaven is above all. ³² He testifies to what He has seen and heard, yet no one accepts His testimony. ³³ Whoever accepts His testimony has certified that God is truthful. ³⁴ For the One whom God has sent speaks the words of God, for God gives the Spirit without limit. ³⁵ The Father loves the Son and has placed all things in His hands. ³⁶ Whoever believes in the Son has eternal life. Whoever rejects the Son will not see life. Instead, the wrath of God remains on him.

The chapter ends by lifting our eyes once more to the One who comes from above, for He alone speaks from firsthand sight of heaven, and to accept His word is to set our seal to it that God is truthful. The Father has poured out the Spirit upon Him without limit and has placed all things into His hands, and beneath it all lies the deepest ground of everything: the Father loves the Son. Then verse 36 closes with the same two destinies once more, now as stark as Scripture anywhere states them. The one who believes already has eternal life, here and now, while the one who refuses the Son will not see life, and the wrath of God remains upon him, that abiding condition which the Son came down to lift. So the chapter that began in the dark ends with everything a person has riding on what he will do with the Son who was lifted up.

Study notes Going deeper

The new birth is something done to you, and never something done by you. Ezekiel had promised it long before, and Jesus expects the teacher of Israel to recognize it when he hears it. And the way into that birth is finally a look, a look toward the Son who was lifted up.

"I will also sprinkle clean water on you, and you will be clean. I will cleanse you from all your impurities and all your idols. I will give you a new heart and put a new spirit within you; I will remove your heart of stone and give you a heart of flesh. And I will put My Spirit within you and cause you to walk in My statutes and to carefully observe My ordinances." Ezekiel 36:25–27 (BSB)

When Jesus speaks of being “born of water and the Spirit” in 3:5, He is almost certainly echoing this very promise, in which cleansing water and a new Spirit come together to make a wholly new heart.

"Make a fiery serpent and mount it on a pole. When anyone who is bitten looks at it, he will live.” So Moses made a bronze snake and mounted it on a pole. If anyone who was bitten looked at the bronze snake, he would live." Numbers 21:8–9 (BSB)

The image is jarring and exact all at once. The very thing that was killing them became, once it was lifted up, the means of their life, for everyone who simply looked. So it is with Christ, who was made sin for us and lifted upon a cross, and who becomes life for all who look to Him in faith. He is not a ladder for us to climb, but a sight for us to behold.