John 3:1 - Meaning and Application

At the close of the previous chapter, we saw that only a few people in Jerusalem were brought to Christ. Yet one important man did come, and that shows the value of laboring even for one soul. It is worth going a long way if one soul may be saved.

This man was Nicodemus. He was one of the Pharisees, a learned scholar, so let no one say that all of Christ’s followers were uneducated men. The ideas of the Pharisees were very different from the spirit of Christianity, yet some of them were brought to bow to Christ. Christ’s grace can overcome even strong resistance. Nicodemus was also a ruler of the Jews, a member of the great Sanhedrin, the highest Jewish council, like a senator and chief adviser in Jerusalem. Even in those bad times, there were some rulers who were favorably inclined to Christ, though they could do little good because most people around them were against them.

Nicodemus came to Jesus by night. He did come privately, not content with hearing public teaching. He wanted to speak with Christ alone, where he could be open and free. Private talk with faithful and wise ministers about the state of our souls can be very helpful (Malachi 2:7). He also came by night as a matter of prudence. Christ had spent the day in public work, and Nicodemus would not interrupt him. He waited for a time when Jesus was free. In this way, private needs must yield to public duties, and the greater good should come before the lesser. Since Christ had many enemies, Nicodemus also came quietly, so the chief priests would not be more stirred up against him.

His coming by night may also show zeal. Nicodemus was a busy man, and perhaps he could not spare time during the day. So he chose to use his evening rest for seeking truth. While others were asleep, he was seeking knowledge, like David who meditated in the night (Psalm 63:6; Psalm 119:148). It was likely the very next night after he saw Christ’s miracles, and he did not want to delay responding to what he had seen. He did not know how soon Jesus might leave town, so he would lose no time. At night, he could speak more freely and face less interruption. These were Christian nights, far better than the learned but worldly nights of the Greeks.

Yet his coming by night may also show fear and shame. He may have been afraid to be seen with Christ, since religion was not popular and rulers often cared too much about appearances. There have always been many hidden followers like that, especially among leaders. Even so, Christ welcomed Nicodemus. He accepted his sincerity and overlooked his weakness. He understood Nicodemus’s timid nature and the pressure of his position. This teaches Christ’s ministers to meet people where they are and to encourage small beginnings, even when they are weak. Later, Nicodemus did own Christ openly when the time came (John 7:50; John 19:39). A small beginning of grace can grow into something much larger.

Nicodemus did not come to talk about politics, even though he was a ruler. He came about the needs of his own soul and its salvation. He went straight to the point and called Jesus “Rabbi,” meaning teacher and a person of honor. That shows respect for Christ. There is hope for those who honor Christ in their speech and attitude. He said, “We know that you are a teacher come from God.” He was saying that Jesus was not trained or sent by men like other teachers, but came with divine authority. The one who would be King first came as a teacher, because he rules by truth, not by force. The world was full of ignorance and error, and the Jewish teachers had become corrupt, so God sent help in time.

Nicodemus also said, “We know,” not only “I know.” He spoke as though others had the same conviction. Perhaps some other Pharisees and rulers had similar thoughts, though they were not brave enough to say so. Or he may have used “we” because he had brought friends or students with him to learn from Jesus. In effect, he was saying, “Master, we come to be taught. We are ready to be your students, because we are sure you are a teacher from God.”

The reason for his confidence was this: “No one can do these signs that you do unless God is with him.” This confirms that Christ’s miracles were real, not fake. Nicodemus was a thoughtful, careful man with every chance to examine them, and he was fully convinced. The miracles even moved him to go against his own interests and against the opinions of his fellow rulers. These signs also point us to the right conclusion: Jesus must be received as a teacher sent from God. His miracles were his credentials. Only the God who rules nature could change nature’s course, and we know that God of truth would never stamp a lie or a trick with his approval.

From there, Christ and Nicodemus began their conversation, or rather, Christ began to preach to him. This may be a summary of Christ’s public teaching as well (John 3:11, 12). In this meeting, Jesus speaks of four things. He begins with the necessity and meaning of regeneration, or the new birth (John 3:3-8).

Jesus answered Nicodemus in a way that fit his address very well. He did, in effect, rebuke what was lacking in Nicodemus’s approach. It was not enough to admire Christ’s miracles and admit that he had come from God. Nicodemus expected the Messiah’s kingdom to appear soon, and he likely imagined it in outward power and glory. Since Jesus did these miracles, Nicodemus seemed to think he might be the Messiah or at least his prophet, so he came to pay him respect and perhaps secure a place in that kingdom. But Christ told him that no one can benefit from that new order unless his spirit, principles, and desires are changed as fully as if he were born again.

Nicodemus had come by night, but that would not do, as Dr. Hammond says, if his religion stayed hidden from others. Or, if we take it another way, Jesus was answering the real purpose behind his visit. When Nicodemus called Christ a teacher sent from God, with an extraordinary message from heaven, he was clearly showing that he wanted to know that message and was ready to receive it. Christ then declared it plainly.

Our Lord Jesus said it with great solemnity: “Truly, truly, I say to you.” He, the Amen, the faithful and true witness, spoke it as an unchangeable truth. Unless a person is born again, he cannot see the kingdom of God. He said this even to Nicodemus, a Pharisee and a teacher in Israel.

What is required is to be born again. That means, first, that we must begin a new life. Birth is the start of life, and to be born again is to start over, after living wrongly or for the wrong ends. We must not try to repair the old building. We must begin at the foundation. Second, we must receive a new nature, with new principles, new affections, and new goals. The word can mean both “again” and “from above.”

We must be born anew, as the word is used in (Galatians 4:9) and (Luke 1:3). By our first birth, we are corrupt, shaped by sin and wrongdoing. So we need a second birth. Our souls must be formed and made alive again. We must also be born from above, as the word is used in (John 3:31) and (John 19:11). That is likely the main sense here, though it does not leave out the other. To be born from above means that this new birth comes from heaven (John 1:13) and leads to heaven. It is a birth into a divine and heavenly life, a life of fellowship with God and the world above. To live that life, we must share in a divine nature and bear the image of the heavenly.

This new birth is absolutely necessary. “Unless a man,” that is, anyone who shares human nature and its corruption, “is born again, he cannot see the kingdom of God,” the kingdom of the Messiah, begun in grace and completed in glory. Unless we are born from above, we cannot see it. That means, first, we cannot understand it. The things of God are such that the natural person must be remade into a spiritual person before he can receive and understand them (1 Corinthians 2:14). Second, we cannot receive its comfort. We cannot expect any benefit from Christ and his gospel, or have any share in it.

Regeneration, or new birth, is absolutely necessary for our happiness now and forever. If we think about what we are by nature, corrupt and sinful, what God is, and what heaven is, it becomes clear that we must be born again. We cannot be happy unless we are holy (1 Corinthians 6:11, 1 Corinthians 6:12). Once this great truth was laid down with such seriousness, Nicodemus objected.

He asked, “How can a man be born when he is old?” He meant, how can someone as old as I am be born again? Can he enter his mother’s womb a second time and be born? This showed, first, his weakness in understanding. He took what Christ said in a physical, worldly way, as if the soul could only be renewed by making the body over again. He seems to have valued himself, like other Jews did, on his first birth and its honors and privileges, perhaps on his birthplace, his family, and his status. So it was a surprise to hear that he needed to be born again. They thought a Gentile convert was like someone born again, but they could not imagine how a Jew, and especially a Pharisee, could need such a thing. Proud people find it hard to accept a new birth.

Second, Nicodemus also showed a willingness to be taught. He did not turn away because the saying was hard. He honestly admitted that he did not understand it, which shows that he wanted more light. When we come across hard things in God’s truth, we should keep attending to the means of knowledge with humility and effort, until God makes them clear to us.

Jesus then took the chance to repeat and confirm what he had said: “Truly, truly, I say to you,” the very same thing as before. God’s word is not uncertain, saying one thing and then another. What he has said, he will stand by, no matter who argues against it. He will not take back his words because people are ignorant or mistaken. Even though Nicodemus did not understand the mystery of regeneration, Christ still affirmed its necessity as clearly as before. It is foolish to try to escape the demands of the gospel by saying they are hard to understand (Romans 3:3, Romans 3:4).

From Nicodemus’s objection, Jesus went on to explain more fully what he meant by regeneration.

The one who brings about this blessed change, and the one who works it, is the Holy Spirit. To be born again means to be born of the Spirit (John 3:5-8). This change does not come from our own wisdom or strength, but from the power and influence of the Holy Spirit, the Spirit of grace. It is the sanctifying work of the Spirit, that is, his work of making us holy (1 Peter 1:2), and the renewing of the Holy Spirit (Titus 3:5). He works through the word he inspires, and he has access to the heart he intends to change.

The nature of this change is also important. It makes a person spiritual, not merely outwardly religious, but inwardly renewed. Those who are regenerated are refined from the dross and waste of fleshly living. The mind and desires of the rational, immortal soul take back the rule they should have over the body. The Pharisees, Jewish religious leaders who focused on outward purity and outward actions, would need a very great change indeed. For them, becoming spiritual would be nothing less than a new birth.

Christ also shows the necessity of this change. It is necessary by the very nature of the case, because no one is fit to enter the kingdom of God until born again: “That which is born of the flesh is flesh” (John 3:6). Here is our sickness, along with its cause, and there is no remedy except new birth. We are flesh, not only in the sense that we have bodies, but also in the sense that we are corrupted by sin (Genesis 6:3). The soul remains a spiritual being, yet it becomes so tied to the flesh, so ruled by fleshly desires, and so busy making provision for the flesh, that Scripture often calls the person fleshly.

How did we come to be this way? We were born of the flesh. This corruption is in us from birth, so if we are to receive a new nature, we must be born again. The corrupt nature, called flesh, comes from our first birth. Therefore the new nature, called spirit, must come from a second birth. Nicodemus had spoken of going back into his mother’s womb and being born again, but even if that were possible, it would not solve the problem. If a person were born a hundred times from the same source, the result would still be flesh, and a clean thing cannot come from what is unclean. He needs a different beginning. He must be born of the Spirit, or he cannot become spiritual.

In short, God made man with both body and soul. At first, the spiritual part ruled the body, so man was called a living soul (Genesis 2:7). But when man gave in to the appetite of the flesh and ate the forbidden fruit, he handed the soul’s rightful rule over to sinful desire. In that sense, he became flesh. The living soul became dead and inactive. “Dust you are” became his condition. In that fallen state, he passed on to his children a human nature that was already corrupted and spoiled. That corruption still spreads through the human race. Sin is woven into our nature; we are shaped in iniquity. For that reason, our nature must be changed. It is not enough to wear a new coat or put on a new face. We must put on the new person. We must become new creatures.

Christ also makes this necessity plain by his own word: “Do not be surprised that I said to you, You must be born again” (John 3:7). Christ has said it, and since he will never take it back, no one can rightly deny it. He is the great Lawgiver, whose will is law. He is also the great Mediator, that is, the one who brings God and sinners together under the new covenant. He has full authority to set the terms of our peace with God and our happiness in him. He is the great Physician of souls, who knows our condition and what our cure requires. He has said, “You must be born again.” He said this to Nicodemus, but it applies to everyone. It is not only for ordinary people, but also for rulers and teachers in Israel.

We should not be shocked by this. When we think about the holiness of the God we deal with, the great purpose of redemption, the corruption of our nature, and the nature of the happiness held out to us, we should not think it strange that so much weight is placed on this one necessary thing.

Christ explains this change with two comparisons. First, the Spirit’s regenerating work is compared to water (John 3:5). To be born again is to be born of water and of the Spirit, meaning of the Spirit working like water. This is like the phrase “with the Holy Ghost and with fire” (Matthew 3:11), where the Holy Spirit is likened to fire.

The main point is that the Spirit, when he makes a soul holy, cleanses and purifies it like water. He removes the dirt that made it unfit for God’s kingdom. This is the washing of regeneration (Titus 3:5). “You were washed” (1 Corinthians 6:11). See also (Ezekiel 36:25). The Spirit also cools and refreshes the soul, as water refreshes a hunted deer or a weary traveler. The Spirit is compared to water again in (John 7:38-39) and (Isaiah 44:3). In the first creation, the life of the waters came from above (Genesis 1:20), and perhaps that is why those who are born from above are said to be born of water.

Christ likely also had baptism in mind, since John had used it and Christ had begun to use it. “You must be born again of the Spirit,” and this inward renewal by the Spirit is shown outwardly in washing with water as the visible sign of spiritual grace. This does not mean that everyone who is baptized is saved, or that only baptized people are saved. But without that new birth, which the Spirit works and baptism signifies, no one will be counted among the protected and privileged people of the kingdom of heaven. The Jews cannot share in the blessings of the Messiah’s kingdom, for which they had long waited, unless they stop expecting to be justified, that is, counted right with God, by keeping the law, and submit to the baptism of repentance, the great gospel duty tied to the forgiveness of sins, the great gospel gift.

Second, this change is compared to wind: “The wind blows where it wishes, and so it is with everyone who is born of the Spirit” (John 3:8). The same word can mean both wind and Spirit. The Spirit came on the apostles with a rushing mighty wind (Acts 2:2). His strong work on sinners’ hearts is compared to the breath of wind (Ezekiel 37:9), and his sweet work on saints’ souls is compared to the north and south wind (Song of Solomon 4:16). This comparison shows that the Spirit works freely, as a free agent. The wind blows where it wishes, not where we direct it, and not under our command. God directs it, and it carries out his word (Psalm 148:8). In the same way, the Spirit gives his influence where, when, on whom, and in what measure he pleases, dividing to each person as he wills (1 Corinthians 12:11).

Jesus’ teaching is powerful, and its effects can be seen plainly. You may not see the hidden cause, but you can hear the result. When a person begins to grieve over sin, feel the weight of inner corruption, long for Christ, and cry, “Abba, Father,” then you can hear the Spirit at work. Then it is like the words about Saul, later the apostle Paul: “Look, he is praying” (Acts 9:11).

The Spirit also works in hidden and mysterious ways. We cannot tell where he comes from or where he goes. How he gathers strength and how he uses it is a mystery to us, and so are his methods. “Which way did the Spirit go?” asked one old text (1 Kings 22:24). See also (Ecclesiastes 11:5) and compare it with (Psalm 139:14).

Christ now turns to the certainty and greatness of gospel truth, using Nicodemus’ weakness as the occasion. Nicodemus still objects, “How can these things be?” (John 3:9). Christ’s explanation of the need for new birth does not seem to make the matter clearer to him. The corruption of human nature, which makes new birth necessary, and the Spirit’s work, which makes it possible, are both mysteries to him.

Though Nicodemus had admitted that Christ was a teacher sent from God, he did not want to accept teaching that clashed with his own ideas. Many people still do this. They say they accept Christ in general, but they will not believe his truth or obey his commands any farther than they like. They want Christ as their teacher, as long as they can choose the lesson.

Nicodemus admits that he does not understand what Christ means. “How can these things be?” In other words, “I do not understand this. My mind cannot reach it.” In this way, the things of God seem foolish to the natural person. Such a person is not only far from them, so they seem dark, but also against them, so they seem foolish.

Because the teaching seems beyond him, Nicodemus begins to question whether it is true. Since it felt impossible to him, he treated it as if it were impossible in itself. Many people think so much of their own understanding that they assume anything they cannot believe cannot be proved. In this way, they miss Christ by their own supposed wisdom.

Christ rebukes Nicodemus for his dullness and ignorance: “Are you a teacher in Israel, and yet you do not know these things?” A teacher in Israel should have known the doctrine of new birth, at least from the Old Testament. This is a warning to those who teach others while they themselves are ignorant of the word of righteousness. It also warns those who spend their time on ideas, ceremonies, small questions, and word studies, while neglecting what changes the heart and life.

Christ’s rebuke also points to the place where Nicodemus lived, in Israel, where he had abundant help for learning, and where God’s revelation was given. He could have learned this from the Old Testament. It also points to the great things he did not know, these necessary things, these divine things. Had he never read (Psalm 50:5, Psalm 50:10), (Ezekiel 18:31), or (Ezekiel 36:25, Ezekiel 36:26)?

Christ then speaks about the certainty and greatness of gospel truth, to show how foolish it is to reject it and to encourage us to search it out (John 3:11-13). The things Christ taught were completely certain. “We speak what we know.” He speaks with full knowledge, not guesswork. Some take “we” to include the witnesses with him on earth, such as the prophets and John the Baptist. Others take it to include the witnesses from heaven, the Father and the Holy Spirit. In either case, the point stands: Christ’s truth is fully reliable.

We have every reason to trust Christ’s words and stake our souls on them. He is not only a truthful witness, one who would not deceive us, but also a fully qualified witness, one who could not be deceived himself. He testified to what he had seen. He did not speak by hearsay, but from the clearest knowledge. What he taught about God, the unseen world, heaven and hell, and God’s will toward us was what he knew. He had been with the Father, as one brought up beside him (Proverbs 8:30).

The unbelief of sinners is made worse by this certainty. The truth is so clear, and yet people still refuse the witness. Many do not believe what they have no real ground to doubt, even though the reasons to trust it are strong.

Christ’s teaching is also very high and heavenly, even when he speaks in plain words drawn from ordinary life. “If I have told you earthly things,” he says, meaning that he has used earthly images, like new birth and the wind, to make divine truth easier to understand, “and you do not believe, how will you believe if I tell you heavenly things?” If simple comparisons are a stumbling block, how much harder would it be if he spoke in pure spiritual terms, without any familiar pictures?

From this we should admire the height and depth of Christ’s teaching. The gospel is a great mystery of godliness. Its truths are heavenly, beyond the reach of human reason and far beyond its discoveries. We should also thank Christ for his kindness in lowering his speech to our level. He speaks to us as to children. He knows our nature, that we are earthly, and our place, that we live on the earth. So he gives spiritual truth through visible things, making it easier and more familiar to us. He does this in parables and in sacraments. At the same time, we should grieve over the corruption of our nature and how unfit we are to receive and welcome Christ’s truth.

Earthly things are despised because people think they are plain and low. Heavenly things are despised because people think they are hard to understand. No matter what method is used, some fault will always be found with it (Matthew 11:17). Yet wisdom will still be shown to be right by her children.

Our Lord Jesus, and he alone, was fit to reveal a doctrine this sure and this high. “No one has gone up into heaven except the one who came down from heaven, the Son of Man” (John 3:13). First, only Christ was able to show us God’s will for our salvation. Nicodemus spoke to Christ as a prophet, but he needed to know that Christ is greater than all the Old Testament prophets, because none of them had gone up into heaven. They wrote by the Holy Spirit, not from their own direct knowledge; see (John 1:18). Moses went up into the mountain, but not into heaven. No one has gained the sure knowledge of God and heavenly things that Christ has; see (Matthew 11:27). It is not for us to send to heaven for instruction. We must wait to receive the instruction heaven sends to us; see (Proverbs 30:4) and (Deuteronomy 30:12).

Second, Jesus Christ is able, fit, and fully qualified to reveal God’s will to us, because he is the one who came down from heaven and is in heaven. He had said, “How will you believe if I tell you about heavenly things?” (John 3:12). Now he gives them an example of those heavenly things when he speaks of one who came down from heaven and is the Son of Man, and yet is in heaven. If the new birth of the human soul is such a mystery, what must the incarnation, Christ becoming human, be like? These are truly divine and heavenly things. Here we get a hint of Christ’s two distinct natures in one person. He has a divine nature, by which he came down from heaven, and a human nature, by which he is the Son of Man. And these two are united, so that while he is the Son of Man, he is also in heaven.

He also gives proof that he can speak about heavenly things and lead us into the hidden truths of the kingdom of heaven. He does this by saying, first, that he came down from heaven. The way between God and man was opened above, not here on earth. The first move toward it did not come from this world, but from heaven. We love him, and we turn to him, because he first loved us and came to us. This points to Christ’s divine nature. The one who came down from heaven is certainly more than a mere man, because he is the Lord from heaven (1 Corinthians 15:47). It also shows his close knowledge of God’s plans, because he came from the court of heaven and had lived in those counsels from eternity. And it shows God making himself known. In the Old Testament, God’s help is described as hearing from heaven (2 Chronicles 7:14), looking from heaven (Psalm 80:14), speaking from heaven (Nehemiah 9:13), and sending from heaven (Psalm 57:3). But the New Testament shows God coming down from heaven to teach and save us.

That he came down in this way is a deep mystery, because God cannot change places, and he did not bring his body from heaven. Yet his coming down in mercy for our rescue is an even greater wonder, because in this he showed his love. Second, he is the Son of Man, the Son of Man spoken of by Daniel (Daniel 7:13), whom the Jews understood to be the Messiah. By calling himself the Son of Man, Christ shows that he is the second Adam, since the first Adam was the father of mankind. Of all the Old Testament names for the Messiah, he chose this one because it best showed his humility and fit his lowly state.

Third, he is in heaven. At that very time, while speaking with Nicodemus on earth, he was still in heaven as God. The Son of Man, as a human being, was not in heaven until his ascension. But the one who is the Son of Man was then, by his divine nature, everywhere present, and especially in heaven. In the same way, the Lord of glory, as such, could not be crucified, and God, as such, could not shed blood. Yet the person who was the Lord of glory was crucified (1 Corinthians 2:8), and God purchased the church with his own blood (Acts 20:28). The two natures are so closely united in one person that what belongs to either nature may be spoken of the one person. He does not say that he was in heaven only in the past, but that he is the one who is in heaven.