Shining light into Nicodemus’ Heart

We all know John 3:16.
We see it proclaimed on coffee cups, bookmarks, T-shirts, bags, golf caps, and signs outside churches. It might even be on your front page of your bible. John 3:16 is one of the best known verses of the Bible among both Christians and non-Christians. says that it’s is the most read verse on their website! So, what more can we learn from this verse? Surely we know it well enough?

Let’s dig deeper into this well-known verse, and see how it sheds light on the gospel as a whole. Maybe there’s more for us to learn. 

1- Jesus Sees.

Chapter 3 starts with the well-known conversation between Nicodemus and Jesus. It’s interesting to note that back at the end of chapter 2, John has written about Jesus seeing what’s inside the heart of man right before Christ’s conversation with Nicodemus. This tells us that when Jesus meets a person, he sees beyond what we can see. Nicodemus is described here as the Pharisee, a religious ruler of the Jews. What do we know about the Pharisees? One thing is that Pharisees were known for their focus on the outward appearance and behaviour rather than the condition of the heart. This becomes clearer when we see what Jesus thought of the Pharisees.

In Matthew chapter 23, Jesus refers to the Pharisees in strong words:

“Woe to you, scribes and Pharisees, hypocrites! For you clean the outside of the cup and the plate, but inside they are full of greed and self-indulgence. You blind Pharisee! First clean the inside of the cup and the plate, that the outside also may be clean. “Woe to you, scribes and Pharisees, hypocrites! For you are like whitewashed tombs, which outwardly appear beautiful, but within are full of dead people's bones and all uncleanness. So you also outwardly appear righteous to others, but within you are full of hypocrisy and lawlessness.” 

Let’s take a look at the dynamics of this conversation between Nicodemus and Jesus. We don’t know exactly what Nicodemus was like as a person. Scripture tells us he was a Pharisee, but obviously every Pharisee was different. But what we do know is that Jesus sees what’s inside of a man. Jesus knew exactly the condition of Nicodemus’ heart, just as He knows what lies in each one of our own hearts. 

Unlike Jesus however, Nicodemus only saw the external appearance. (Just like us, in fact). He came from earth and not from heaven. He didn’t see that Jesus - the man he was having a conversation with - is actually God incarnate. In Nicodemus’ earthly eyes, Jesus was only a teacher.

Nicodemus – like the rest of the nation of Israel - was waiting for the arrival of a Messiah that would fulfill his expectations. He was waiting for a Savior to rescue his nation from earthly oppression and human bondage. Nicodemus didn’t see that the greatest rescue they needed was from their own sin. So here we have Nicodemus with his earthly concerns, facing Jesus who searches mind and heart (Rev 2:23). Even before a word was on Nicodemus’ tongue, Jesus knew it (Psalm 139:4). Jesus knew exactly what to say to Nicodemus, and this helps us to understand his answer.

Let’s look at verse 3 of John 3. Jesus answered, “Truly, truly I say to you, unless one is born again, he cannot see the kingdom of God.”

Straight away Jesus pushes past the outward appearance, and addresses the real problem that Nicodemus - this apparently righteous man - was actually facing: the problem of sin. 

Because Jesus sees beyond what our physical eyes see. He sees that Nicodemus (like us) needs to be transferred from one domain to another. Colossians 1:13 describes believers as having been “delivered from the domain of darkness and transferred to the kingdom of his beloved Son.” Jesus saw Nicodemus still in this domain of darkness and he needed to be born into a new Kingdom. Simply put, that’s what it means to be born again: dying to one kingdom and being born anew into another. 

But how do we enter this new Kingdom? Let’s think about the phrase ‘Kingdom of God’. It naturally implies that there is a King. Entering the Kingdom of God means that we acknowledge the King who is on the throne. We were all created in the image of God to reflect His character and spread His glory under His rule. But – by our sin - we have all rejected His rule, therefore we are outside of this Kingdom of God. The Bible calls our condition spiritually dead, blind, alienated from the life of God, destined to perish, with the wrath of God remaining on us. This is truly the domain of darkness; it’s about spiritual blindness of human nature. 

Consider Nicodemus for a moment. He would have had much authority, and would have been well respected. That is, if we only look at his outward appearances and measure him by the standards of man. He would have appeared, humanly speaking, to have been a very righteous man. But here he is talking with Jesus Christ, in whom there is no sin (1 Peter 2:22). Jesus is the radiance of the glory of God and the exact imprint of his nature, and he upholds the universe by the word of his power.(Hebrew 1;3) And his word is like a two-edged sword, piercing to the division of soul and of spirit, of joints and of marrow, and discerning the thoughts and intentions of the heart. (Hebrew 4:12) He is Jesus. 

The conversation between Jesus and Nicodemus continues to unfold in verse 4. Nicodemus’ answer to Jesus suggests that he doesn’t understand what Jesus meant. He is not aware of where he stands, in the domain of darkness. He cannot see spiritual truth. Just because he is a teacher of the law given by God, and rules “God’s people”, it doesn’t automatically mean he belongs to the Kingdom of God. As Jesus says, “born of the flesh is flesh, born of the Spirit is Spirit” (verse 6). 

So what does this conversation have to do with us, 2000 years later? One of the things it tells us is that our religious background, our education, and our moral standards have no influence on our standing in the Kingdom of God. No one is ahead of anyone else. Just as Nicodemus – an esteemed teacher of holy law – had not earned a place on the Kingdom of God, none of us have earned a place in this Kingdom by our works or religious activity. I myself was born and grew up in Japan, a Buddhist and animist country. But my sisters from “Christian” countries have no advantage or head start when it comes to salvation. To enter the Kingdom of God, each one of us needs the work of God in our hearts. The Old Testament carries many prophecies that reveal the work that God (not us) was going to do in the coming days, to bring people into his Kingdom. Ezekiel 36:25-27 says:

“I will sprinkle clean water on you, and you shall be clean from all your uncleanness, and from all your idols I will cleanse you. And I will give you a new heart, and a new spirit I will put within you. And I will remove the heart of stone from your flesh and give you a heart of flesh. And I will put my Spirit within you, and cause you to walk in my statutes and be careful to obey my rules”.

Notice that the cleansing, the giving of the new heart, the causing of us to walk in his statutes – this is all the work of God.

As we think about Nicodemus being unaware of the heavenly things and locked into an earthly view of reality, can we see this reflected in our lives? Unless we see what Jesus sees - which is our standing before God - we don’t know what it means to be in need of a new heart. And when we understand where we are before this Holy God, we will truly seek His salvation and deliverance. I wonder if you have seen where you stand. When we see our offenses in light of God’s holiness, we have deep sorrow over our sin. This is a good place to be because “godly grief produces a repentance that leads to salvation without regret, whereas worldly grief produces death.” (2 Corinthians 7:10).

Do you see the measure of your sins and do they sadden you? Do you sincerely desire to wash them away? Jesus says in verse 5, explaining how we become born again, “unless one is born of water and spirit, he cannot enter the kingdom of God.” Water was symbol of purifying of our hearts. Scripture tells us that “If we confess our sins, he is faithful and just to forgive us our sins and to cleanse us from all unrighteousness. If we say we have not sinned, we make him a liar, and his word is not in us.” (1 John 1:9-10) 

It is possible - just like Nicodemus and his fellow Pharisees - to see the external appearance but not to see our need of heart change. Having knowledge of Jesus and acknowledging Him as your own King are two different things. The Bible teaches us that we need more than having knowledge of Him – we actually need to acknowledge Him. This means not just knowing about Him, but submitting to Him and His rule. When we do that, the bible uses the analogy of a wind blowing. We cannot see the wind, but can see the effects of the wind. In the same way, our life shows whether Jesus rules it or not. Are you born again into this Kingdom? Is Jesus increasing in your lives? 

For some reading this, the fact Jesus sees through to our hearts might not sound like good news, but it is! That’s because God didn’t leave us in darkness. He provided the way for us to be transferred from one domain into another. Let’s look in detail what God has done to rescue our ‘Nicodemus heart’. 

2 - God acts

Let’s look at verse 16-17 of John 3. The good news is that although God sees our condition inside out, he didn’t condemn the world. Instead, he acted on the situation by sending His Son to die. Do you remember the woes to the Pharisees we read earlier? There is righteous anger towards our sins, yet Jesus patiently explains to spiritually blind Nicodemus the process of entering the Kingdom of God. “God doesn’t desire anyone to perish, but desire all to reach repentance.” (2 peter 3:9). Jesus knows indeed that he came to seek and save the lost. And he became our substitute on the cross, to bear the weight of sin of anyone who believes in him. This entrance into the Kingdom is offered to everyone, irrespective of background, country, and age. He offers his rescue because we are all in need of it. How amazing is His love for us? 

God is rightfully offended by his creatures’ rebellion, and yet he sent his only son, so that we may receive eternal life instead of perishing. Jesus became sin for us, and that means the wrath of God that is set against us because of our sins, has fallen upon our sinless Savior Jesus Christ. This is so that we may see and enter the Kingdom of God and worship the King forever. He is such a compassionate, patient, loving God, and yet we also see His justice and holiness not compromised in His son’s death. A sinless one needed to die in order to save many, and God himself came for that rescue in Jesus Christ. This is our God. 

So those of us who are filled with guilt, fear, regret and worry over our sins, let us take heart and behold Jesus, who came in the glory of God himself, yet died as criminal for those sins you may be even anxious about right now. In the words of the famous hymn, “It is Well with my Soul”:

“My sin - not in part but the whole -
Is nailed to the cross, and I bear it no more,
praise the Lord, praise the Lord, O my soul!”. This crucified Jesus was raised again, and now he is seated at the right hand of God in heaven, calling many to himself. This is truly wonderful news!

And it’s a solution that man could not have come up with. A human solution to sin would be to simply “try harder”. We see this in almost every other religion. Work harder and harder to achieve some kind of moral righteousness on your own strength, willpower and sheer hard work. It’s tiring and never-ending. The Gospel is not human invention but God’s wisdom. Not a work of flesh, but the work of the Spirit of God. 

3 – We must respond.

When we are presented with such a proclamation, the Bible doesn’t give us the option to walk away without any response. In fact, the Bible is clear that there are only two possible ways to for us to respond. Look at verse 18. We can either believe in Christ or not believe in him. The consequences of believing and not believing are also clear.
Scripture tells us that “Whoever believes in the Son has eternal life; whoever does not obey the Son shall not see life, but the wrath of God remains on him.” (Everyone knows John3:16, but how many of us also know John 3:36?)

Just as the bites of the fiery serpent were deadly, sin is deadly. Unless you see the Son, you will not see life.

We’ve seen that receiving eternal life – being transferred from the domain darkness into the Kingdom of God - is not by our works, or our background credentials, but by faith alone in the reconciliation provided by the Son of God. Have you put your faith in Him to forgive and cleanse you of your sins?

2 Corinthians 4:6 tells us that “God, who said, “Let light shine out of darkness,” has shone in our hearts to give the light of the knowledge of the glory of God in the face of Jesus Christ.”

God opens our eyes to see the glory of Christ as the only Son of God. Seeing Jesus is like receiving the light of the knowledge of the glory of God. That sight of His glory gives us faith, and faith gives us life. This is the pattern that John writes, over and over again. Here it is again in John 20:31. “these are written so that you may believe that Jesus is the Christ, the Son of God, and that by believing you may have life in his name.” Have you seen his glory? Have you put your trust in him? Then you are born again to have life in His name. 

This sight of Jesus and his glory is not only for those who are still in darkness. Even after putting our trust in him, we might find that our doubts, worries, fear, selfishness, and pride can cloud our vision of His glory. This is where the community of believers in the body of Christ comes in. We corporately adjust our sight of him by reading Scripture together, studying, singing, celebrating communion and baptisms, serving and reminding each other to keep beholding the glory of Christ. This is how we move from one degree of glory to another. To be conformed to the image of Christ, to reflect God’s glory as originally intended for us at the time of creation.

As we conclude, and in light of what we have seen, I would like to suggest a few questions that we could ask ourselves in order to apply these truths. 

1) Am I born again?

Am I tired of constantly trying to please God, hoping that my righteousness and good deeds are good enough to take me to heaven? Have I tried to reach God through my works and efforts, rather than simply trusting in God and believing what he has done for me? Is my heart still like Nicodemus? How can it be, that I must just believe? There must be something I can contribute?

If that’s you, the words of Jesus to Nicodemus are speaking to you: “unless you are born of water and Spirit, you cannot see the kingdom of God.” Stop relying on your own efforts, like Nicodemus. Start trusting in what Christ has already done to draw us to himself.

2) Am I growing in humility, understanding my true condition before God?

If salvation depends entirely on Him, there is no room for us to boast about being a Christian, no matter how long and deeply we have been walking with God. That’s why we need to hear the Gospel again and again, to be reminded from where we were rescued.

3) Am I rejoicing in this salvation?

Jesus tells us in John 15:11 that “These things I have spoken to you, that my joy may be in you, and that your joy may be full.” God causes us to be born again to a living hope to an inheritance that is imperishable, undefiled, and unfading! (1 Peter 1:3) Is my attitude a reflection of such hope?

4) Am I sharing this good news?

In Romans 10, we read ‘How then will they call on him in whom they have not believed? And how are they to believe in him of whom they have never heard?' God causes sinners to be born again by shining light upon Christ, but he uses our words to share this good news. If we believe that Jesus is indeed light and we have everlasting life in his name, we should strive tirelessly to share this light amongst our family and friends.

5) Am I anxious and worried?

When I lose sight of who God is and the nature of his love for me, I become prone to worry and fear. This world is full of suffering of all kinds, full of disappointments, trials, conflicts and uncertainty. We need to fix our eyes on the things above where Jesus, our King is seated at the right hand of God. And praise God, it is possible for those of us who are born again - who are given spiritual eyes - to see the unseen, the eternal things of heaven.

Finally – have you got a John 3:16 bookmark or coffee cup? Needless to say, it’s a loving thing to share John 3:16 in anyway possible. A John 3:16 coffee cup can open up your conversation with your friends. A John 3:16 bookmark likewise. But we need to be careful not to turn the Gospel into just “a lucky charm”. It's God himself. In John 3:16, we see the glory of Christ. If we miss what we are supposed to see, we are missing the main thing. So - Lord Jesus, have mercy on us, and give us sight each day to see you, and have life in your name.

Let us pray.
Dear heavenly Father,
We acknowledge that we are far from you without your grace. But we thank you for loving us, and revealing your love to us by sending your only Son.
May you open the eyes of those who are still in darkness and may you continue to enlighten the eyes of our hearts, which can become blind again and again, so that we may know the hope to which you have called us, and the riches of your glorious inheritance in the saints, and the immeasurable greatness of your power toward us who believe. Thank you for revealing the heavenly things to us who are earthbound. Teach us the full meaning of having life in your name. Fill our hearts O Lord with great joy. We pray this in Jesus’ name. Amen.