Many claim that the Bible has hidden or secret messages or codes. Is this true? Are there secret messages in the Bible? If so, what are they?
The Hidden Mystery
Paul is clear that there are some mysteries in the gospel when he wrote to the Ephesians in 3:3-6 “the mystery was made known to me by revelation, as I have written briefly. When you read this, you can perceive my insight into the mystery of Christ, which was not made known to the sons of men in other generations as it has now been revealed to his holy apostles and prophets by the Spirit. This mystery is that the Gentiles are fellow heirs, members of the same body, and partakers of the promise in Christ Jesus through the gospel.” Here Paul shows that the mystery of Christ has not been known until recently, in his time, and that it was even hidden from him at one point. This mystery was only recently, relatively speaking, been revealed by the apostles, the prophets but not by human means. It was revealed only “by the Spirit” or Holy Spirit of God. Part of the mystery is that salvation is not only for the Jews, which they had formerly believed claiming to be the children of Abraham, but it is now for the Gentiles too. Salvation is not about race, which they had believed, but about grace.
Revealing the Secret Mysteries
Paul was sent  “to preach to the Gentiles the unsearchable riches of Christ, and to bring to light for everyone what is the plan of the mystery hidden for ages” (Eph 3:8b-9). Jesus told the disciples once that “To you it has been given to know the secrets of the kingdom of heaven, but to them it has not been given” (Matt 13:11) which meant it had not been given to the Jewish religious leaders. Jesus acknowledges that these were “the secrets of the kingdom of heaven” that is not given to everyone. He said that “I speak to them in parables, because seeing they do not see, and hearing they do not hear, nor do they understand” (Matt 13:13) but to the disciples and to those who trust in Him He says “blessed are your eyes, for they see, and your ears, for they hear. For truly, I say to you, many prophets and righteous people longed to see what you see, and did not see it, and to hear what you hear, and did not hear it” (Matt 13:16-17). Paul told King Agrippa about his calling and that it is God Who opens the eyes and not man that reveals these hidden mysteries telling the king that the Lord told Paul “I will rescue you from your own people and from the Gentiles. I am sending you to them to open their eyes and turn them from darkness to light, and from the power of Satan to God, so that they may receive forgiveness of sins and a place among those who are sanctified by faith in me” (Acts 26:17-18). God is the One Who must open our eyes because Satan, “the god of this world has blinded the minds of the unbelievers, to keep them from seeing the light of the gospel of the glory of Christ, who is the image of God” (2 Cor 4:4).
Are There Secret Messages in the Bible?
I believe that anything that is hidden is hidden only because a person has refused to humble themselves and repent before God. Jesus says “nothing is hidden that will not be made manifest, nor is anything secret that will not be known and come to light” (Luke 8:17) “for whatever is hidden is meant to be disclosed, and whatever is concealed is meant to be brought out into the open” (Mark 4:22). What might be unseen or not understood can be seen and understood with the Holy Spirit as Paul tells the church at Corinth “a natural man does not accept the things of the Spirit of God, for they are foolishness to him; and he cannot understand them, because they are spiritually appraised” (1 Cor 2:14). This is why “the message of the cross is foolishness to those who are perishing, but to us who are being saved it is the power of God” (1 Cor 1:18). What is hidden or secret can be revealed by God’s Spirit so there are no secret messages that God would ever hide from His own children. He makes evident those things we need to know but for those who have refused to repent and humble themselves, He will not give them His Spirit and without His Spirit, they cannot ever understand the mystery of the gospel. God is not unfair. He will save those who submit to Him in all humility and confess their sins to Him and trust in His One and Only Son, Jesus Christ but to the unbelievers who remain proud and unrepentant, the gospel will remain foolishness to them because they can’t see their need for the Savior. This reflects what James wrote “God opposes the proud, but gives grace to the humble” (4:6). God gives to the humble His Spirit and the understanding of His Word but He is opposed to or resists giving anything to those of a proud mind. God cannot work with those who are full of pride for how can God fill anyone who is already full of themselves?
God is not unfair. He will save those who humble themselves before Him, who bow down to worship Him, to those who repent (turn away) from their sins, who confess them to God and then put their trust in the only Person Who can save them…Jesus Christ  (Acts 4:12). People that believe that there are secret hidden messages are ignoring those things that are plain. The main things are the plain things (e.g. Roman 10:9-13, Acts 4:12, 16:30-31; John 3:16-17) and are so simple that even a child can understand them but the educated and proud cannot because of their pride. Others believe in an alphabetical Bible code that can be understood by the way the words and letters are ordered. Some see the sequences of certain words and letters as giving special meaning or enabling someone to read hidden or secret messages. Nothing could be further from the truth. God speaks through Paul to debunk these myths: “For what can be known about God is plain to them, because God has shown it to them. For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made. So they are without excuse” (Rom 1:19-20). God has made Himself known so disbelievers are without excuse. It is plain to them. The only reason that people deny the existence of God is because they want to hold onto their sin but unless they repent and trust in the Savior, it is no secret that they face the wrath of God on Judgment Day (Rev 20:12-15). These things are not hidden from unbelievers…they are made plain from God, therefore they are surely “they are without excuse.”
To understand the Bible you must start reading, take a look at this related article: How to Find Time to Read the Bible 
Scripture quotations are from The Holy Bible, English Standard Version® (ESV®), copyright © 2001 by Crossway, a publishing ministry of Good News Publishers. Used by permission. All rights reserved.