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John 3:1–21 — Jesus and Nicodemus: Born Again, the Son Lifted Up, and the Light

·15 min read·Dennis Mercado
#bible-study#john#theology#discipleship

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John 3:1–21 — Jesus and Nicodemus

Study Diagram Overview

From my Excalidraw study notes—a visual map of Jesus and Nicodemus, the new birth, the Son lifted up, and the light. Open diagram in full size →

Scene Theme Key idea
Nicodemus comes at night Intellectual affirmation vs. personal transformation Jesus knows the heart (John 2:24–25); later he steps into the light (7:50–51; 19:39–40)
Born again / from above gennēthē anōthen — birth from God Cannot see the kingdom without new birth
Water and Spirit Physical vs. spiritual birth (water: amniotic → limited life / purity → eternal life); bronze laver = ongoing cleansing New creation (2 Cor 5:17); tabernacle typology
Wind and Spirit pneuma / ruach — invisible, sovereign, unseen yet transformative So it is with everyone born of the Spirit
Son of Man lifted up Numbers 21:4–9 — bronze snake Believe in Him → eternal life
John 3:16–21 God gave His Son; light has come Believe or be condemned; come to the light

Key themes in the diagram: Nicodemus as teacher of Israel (arc: night → defense before Sanhedrin → burial with Joseph → stepping into the light) | Born again = from above | Water and Spirit: physical vs. spiritual birth; bronze laver for priestly cleansing | Wind analogy: Spirit’s work as a mysterious, sovereign act of God—unseen yet transformative | Moses lifted up the snake → Son of Man lifted up | God loved the world in this way: He gave His Son | Light and darkness: judgment reveals what we love

Introduction: The Night Visit

John 3 records a conversation between Jesus and Nicodemus, a Pharisee and ruler of the Jews (member of the Sanhedrin). Nicodemus comes at night—a detail that may suggest caution, fear of his peers, or the spiritual darkness that Jesus will address. Later in John, Nicodemus steps into the light: he defends Jesus before the Sanhedrin (7:50–51) and helps bury Him with Joseph of Arimathea (19:39–40). His arc from night to bold association with Jesus illustrates what it means to "come to the light" (3:21). He acknowledges Jesus’ divine authority: "We know that you are a teacher who has come from God, for no one could perform these signs you do unless God were with him." (v. 2, CSB). Yet Jesus immediately redirects the conversation from signs and recognition to the necessity of the new birth. The passage moves from birth from above (vv. 1–8), to the Son of Man lifted up (vv. 9–15), to God’s love and the judgment of light and darkness (vv. 16–21).

Verse-by-Verse Exposition

Verses 1–2: Nicodemus Comes to Jesus

1 There was a man from the Pharisees named Nicodemus, a ruler of the Jews. 2 This man came to him at night and said, "Rabbi, we know that you are a teacher who has come from God, for no one could perform these signs you do unless God were with him."

Notes drawn from your study:

  • Nicodemus: A common name in first-century Palestine. As a "ruler of the Jews" he belonged to the Sanhedrin—the Jewish governing council. He was learned, of elite status, and influential.
  • Came at night: The timing may indicate prudence (avoiding public association) or, in John's symbolism, that he was still in moral and spiritual "night" until he came to the light (cf. 3:19–21).
  • "We know": The "we" is likely plural for Nicodemus and other Sanhedrin members—a corporate, cautious acknowledgment.
  • Intellectual vs. personal: Nicodemus offers an intellectual affirmation of Jesus' authority based on signs, not a confession of need or a plea for personal transformation. Jesus will address the heart, not merely the mind.

▶ Discipleship application: Coming to Jesus with correct doctrine or recognition of His power is not the same as being born again. The Lord looks at the heart (cf. John 2:24–25). We must guard against a faith that affirms Jesus as "teacher from God" while resisting the demand to be transformed by the Spirit.

Verses 3–4: Born Again / From Above

3 Jesus replied, "Truly I tell you, unless someone is born again, he cannot see the kingdom of God." 4 "How can anyone be born when he is old?" Nicodemus asked him. "Can he enter his mother's womb a second time and be born?"

Notes drawn from your study:

  • Why Jesus redirected: Jesus does not build on Nicodemus' compliment. He goes straight to the one thing that matters: entrance into the kingdom requires new birth. Signs and titles do not save; regeneration does.
  • Born again: The phrase translates Greek gennēthē anōthen. Anōthen means "from above" or "from on high"—it is a birth from God, not a second physical birth. Jesus' next words (water and Spirit) make this clear.
  • Cannot see the kingdom: To "see" the kingdom is to perceive it, enter into it, and experience it. Without new birth, a person remains outside no matter how religious or learned.
  • Nicodemus' misunderstanding: He takes "born again" in a literal, physical sense. His question reveals that he is thinking in fleshly terms—Jesus will contrast flesh and Spirit (v. 6).

▶ Discipleship application: The kingdom of God is not entered by learning, status, or moral effort. It requires a birth that only God can give. Ask: Have I rested in Christ for this new birth, or am I still trying to "see" the kingdom by my own credentials?

Verses 5–7: Born of Water and the Spirit

5 Jesus answered, "Truly I tell you, unless someone is born of water and the Spirit, he cannot enter the kingdom of God. 6 Whatever is born of the flesh is flesh, and whatever is born of the Spirit is spirit. 7 Do not be amazed that I told you that you must be born again."

Notes drawn from your study:

  • Born of water and the Spirit: Most likely refers to spiritual birth that cleanses from sin and brings transformation—the Spirit's work of regeneration (cf. Ezekiel 36:25–27: water and Spirit in the new covenant). Some also see a reference to baptism as the sign of this reality; either way, the emphasis is on the Spirit's sovereign work.
  • Flesh vs. Spirit: What is "born of the flesh" (human descent, natural life) remains flesh. It cannot produce spiritual life or qualify anyone for the kingdom. Only the Spirit can give spiritual birth. This underlines monergistic regeneration—God alone gives the new birth.
  • "You" is plural: Jesus may be addressing Nicodemus and the wider group he represents—all must be born again.
  • Physical vs. spiritual birth (diagram): The diagram contrasts physical birth (water as amniotic fluid → limited life with sin) with spiritual birth (water as purity → eternal life). Only the latter qualifies for the kingdom.
  • Tabernacle connection: The bronze laver in the tabernacle stood between the bronze altar and the Holy Place; priests washed their hands and feet in its water before ministering, symbolizing ongoing cleansing after atonement. Spiritual birth involves God's water for cleansing—purity and new life from Him.

Cross-references: Ezekiel 36:25–27; Titus 3:5; 2 Corinthians 5:17 (new creation).

▶ Discipleship application: No one enters the kingdom by bloodline, tradition, or moral improvement. We are utterly dependent on the Spirit's work. Let this humble us and drive us to pray for ourselves and others that God would grant new birth.

Verse 8: The Wind and the Spirit

8 The wind blows where it pleases, and you hear its sound, but you don't know where it comes from or where it is going. So it is with everyone born of the Spirit.

Notes drawn from your study:

  • Wind and Spirit: In both Greek (pneuma) and Hebrew (ruach) the same word can mean "wind," "breath," or "Spirit." Jesus uses the wind as an analogy for the Spirit's work: you cannot see the wind, but you see its effects; you cannot control where it blows. So it is with everyone born of the Spirit—the work is invisible, sovereign, and effectual. It is a mysterious, sovereign act of God like the wind—unseen yet transformative.
  • Spiritual things are spiritually discerned: The natural person does not accept the things of the Spirit (1 Corinthians 2:14). Understanding the new birth requires the Spirit's illumination. Jesus knows where He came from and where He is going (John 8:14); those born of the Spirit have the mind of Christ (1 Corinthians 2:16).

Cross-references: 1 Corinthians 2:13–16; John 8:14; Genesis 1:2 (Spirit hovering).

▶ Discipleship application: We do not manufacture or fully explain the new birth; we testify to it and submit to the Word that the Spirit uses. Do not be discouraged when others "do not understand"—pray that the Spirit would blow where He pleases and bring life.

Verses 9–12: Earthly and Heavenly Things

9 "How can these things be?" asked Nicodemus. 10 "Are you a teacher of Israel and don't know these things?" Jesus replied. 11 "Truly I tell you, we speak what we know and we testify to what we have seen, but you do not accept our testimony. 12 If I have told you about earthly things and you don't believe, how will you believe if I tell you about heavenly things?"

Notes drawn from your study:

  • Jesus' rebuke: Nicodemus is a "teacher of Israel" yet does not grasp the necessity of the new birth—a theme that the Old Testament (e.g., Ezekiel 36; Jeremiah 31) and the Judaism of the day could have prepared him for. Jesus gently but firmly exposes his lack of understanding.
  • We speak what we know: Jesus speaks with divine authority; He and the Father are one in testimony. Rejection of His words is rejection of God's testimony.
  • Earthly things: The new birth, the wind, the contrast of flesh and Spirit—these are "earthly" in the sense that they touch life in this world. If Nicodemus will not believe these, he will not believe "heavenly" things (e.g., the Son's descent from heaven, the cross, eternal life).

▶ Discipleship application: Knowledge of Scripture and religious office do not guarantee spiritual understanding. We need the Spirit to open our eyes. And we must respond to the "earthly" claims of the gospel—sin, repentance, faith, new birth—before we can truly grasp the full glory of heavenly things.

Verses 13–15: The Son of Man Lifted Up

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 so that everyone who believes in him may have eternal life."

Notes drawn from your study:

  • Only the Son has descended from heaven: No human has ascended to heaven to bring down divine revelation. The Son of Man alone has come down from heaven (cf. John 1:18; 6:38). He is the unique revealer and the unique sacrifice.
  • Moses and the bronze snake: In Numbers 21:4–9 the people sinned, were bitten by poisonous snakes, and cried out. God instructed Moses to make a bronze snake and mount it on a pole; everyone who looked at it lived. Jesus is that kind of remedy: He must be lifted up (on the cross—cf. John 8:28; 12:32–33), and everyone who believes in Him (the spiritual "look") will have eternal life.
  • Must be lifted up: The cross is necessary—God's plan of salvation through the atoning death of the Son.

Cross-references: Numbers 21:4–9; John 8:28; 12:32–33; 1:18.

▶ Discipleship application: Eternal life is not by works or birthright but by believing in Him—the one lifted up on the cross. We point people to Christ crucified, as Moses held up the snake in the wilderness. Look and live.

Verses 16–18: God's Love and the Gift of Eternal Life

16 For God loved the world in this way: He gave his one and only Son, so that everyone who believes in him will 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 Anyone who believes in him is not condemned, but anyone who does not believe is already condemned, because he has not believed in the name of the one and only Son of God.

Notes drawn from your study:

  • God loved the world in this way: The love is not mere sentiment but action—He gave His one and only Son. The extent and nature of God's love are defined by the gift of the Son (cf. 1 John 4:9).
  • Everyone who believes: Salvation is offered to all; it is received by faith. "Believes in him" means trust in, reliance upon, the Son.
  • Not perish … eternal life: Two destinies—perish or have eternal life. Belief in the Son is the dividing line.
  • Not to condemn but to save: Christ's first coming was for salvation. Those who do not believe are already condemned—not because God is eager to condemn, but because they have not believed in the name of the one and only Son. The verdict turns on faith in Christ.

Cross-references: 1 John 4:9; Romans 8:1; 5:8.

▶ Discipleship application: We are saved by grace through faith in the Son. There is no middle ground: believe and have life, or refuse to believe and remain under condemnation. Proclaim the gift of the Son and call people to believe in His name.

Verses 19–21: Light, Darkness, and Judgment

19 This is the judgment: The light has come into the world, and people loved darkness rather than the light because their deeds were evil. 20 For everyone who does evil hates the light and avoids it, so that his deeds may not be exposed. 21 But anyone who lives by the truth comes to the light, so that his works may be shown to be accomplished by God.

Notes drawn from your study:

  • The judgment: The decisive factor is the response to the light (Jesus—cf. John 1:4–5; 8:12). The light has come; people loved darkness because their deeds were evil. Judgment is not arbitrary—it reveals what people already chose.
  • Evil and the light: Those who do evil hate the light and avoid it so their deeds are not exposed. They prefer to hide (like Adam in the garden) rather than repent.
  • Truth and the light: Those who live by the truth come to the light. Their works are shown to be accomplished by God—the fruit of grace, not self-glory. This is the mark of the regenerate: they come to the light and acknowledge that their good works are from God.

Cross-references: John 1:4–5; 8:12; 1 John 1:5–7.

▶ Discipleship application: We are either drawn to the light or we hide from it. Coming to the light means honesty about sin and dependence on God. Let us live by the truth and come to the light, and let our lives show that our works are accomplished by God.

Summary: Theological Themes from Your Notes

  1. New birth: Entrance into the kingdom requires birth from above—of water and the Spirit—not flesh or human effort.
  2. Sovereignty of the Spirit: The Spirit works like the wind—sovereignly, invisibly, effectually. Regeneration is God's work.
  3. The Son lifted up: Eternal life is through believing in the Son of Man lifted up (the cross), as in the type of the bronze snake.
  4. God's love and gift: God gave His one and only Son so that everyone who believes in Him will not perish but have eternal life.
  5. Belief and condemnation: Belief in the Son removes condemnation; unbelief leaves people already condemned.
  6. Light and darkness: The light has come; people either come to the light (live by the truth) or love darkness (evil deeds). Judgment reveals that choice.

For Further Study

  • Nicodemus's arc: He approached Jesus secretly at night (3:2), later defended Jesus openly before the Sanhedrin (7:50–51), and helped bury Him with Joseph of Arimathea (19:39–40)—stepping into the light of truth.
  • Bronze snake typology: Compare Numbers 21 with John 3:14–15 and the theme of "looking" and "believing."
  • Water and Spirit in the OT: Study Ezekiel 36:25–27 and Jeremiah 31:31–34 as background for the new birth.

Reflection & Response

How does this shape your walk?

  • New birth: Have you come to Christ for the new birth, or are you relying on learning, tradition, or moral effort?
  • The Spirit: Are you depending on the Spirit's work in your life and in the lives of others, or trying to manufacture spiritual change?
  • The cross: Do you point yourself and others to the lifted-up Son as the only way to eternal life?
  • Light and darkness: Do you come to the light—living by the truth and acknowledging your need—or do you hide from exposure?
  • Mission: Like Jesus with Nicodemus, do you redirect conversations to the necessity of the new birth and faith in the Son?

Documentation compiled from study notes (C3:V1-21) and diagram C3-V1-21. Scripture references from CSB (Christian Standard Bible).