The apostle John writes, "For God so loved the world, that He gave His only Son, so that everyone who believes in Him will not perish, but have eternal life" (John 3:16); yet, in rare instances, the Bible records God as hating Esau as a prerogative of His choice.

The pronouncement of the word of the Lord to Israel through Malachi: "I have loved you," says the Lord. But you say, "How have You loved us?" "Was Esau not Jacob's brother?" declares the Lord. "Yet I have loved Jacob; but I have hated Esau, and I have made his mountains a desolation and given his inheritance to the jackals of the wilderness." Though Edom says, "We have been beaten down, but we will return and build up the ruins"; this is what the Lord of armies says: "They may build, but I will tear down; and people will call them the territory of wickedness, and the people with whom the Lord is indignant forever." And your eyes will see this, and you will say, "The Lord be exalted beyond the border of Israel!" (Mal 1:1-5)

for though the twins were not yet born and had not done anything good or bad, so that God's purpose according to His choice would stand, not because of works but because of Him who calls, it was said to her, "The older will serve the younger." Just as it is written: "Jacob I have loved, but Esau I have hated." (Rom 9:11-13)

The time of the Patriarchs is unique in biblical history. It represents the period when God makes His unilateral and unconditional covenant with Abraham and affirms it with the descendants of Abraham until the formation of the nation of Israel. Esau, the grandson of Abraham and fraternal twin of Jacob, is of the third generation; but, it is with Jacob that God affirms the Abrahamic Covenant (Isaac: Gen 26:2-5, 23-25, Jacob: Gen 28:12-15; 48:3-4).

But what is it that God hates about Esau especially in light of "though the twins were not yet born and had not done anything good or bad, so that God's purpose according to His choice would stand, not because of works but because of Him who calls" (Rom 9:11)? In providing some historical data, the Bible does shed some light to this question.

Esau and Jacob were portrayed as contentious twins from the very beginning:

Esau failed to appreciate the significance and rights of the firstborn and was dishonest in not revealing his oath, selling his birthright to Jacob, to his father:

When Jacob had cooked a stew one day, Esau came in from the field and he was exhausted; and Esau said to Jacob, "Please let me have a mouthful of that red stuff there, for I am exhausted." Therefore he was called Edom by name. But Jacob said, "First sell me your birthright." Esau said, "Look, I am about to die; so of what use then is the birthright to me?" And Jacob said, "First swear to me"; so he swore an oath to him, and sold his birthright to Jacob. Then Jacob gave Esau bread and lentil stew; and he ate and drank, and got up and went on his way. So Esau despised his birthright. (Gen 25:29-34)

When Esau heard the words of his father, he cried out with an exceedingly great and bitter cry, and said to his father, "Bless me, me as well, my father!" And he said, "Your brother came deceitfully and has taken away your blessing." Then Esau said, "Is he not rightly named Jacob, for he has betrayed me these two times? He took away my birthright, and behold, now he has taken away my blessing." And he said, "Have you not reserved a blessing for me?" (Gen 27:34-36)

When God affirms the Abrahamic covenant with Isaac, He places an emphasis on Abraham's obedience to His commandments, statutes and laws (Gen 17:19; 26:4-5). While the Bible does not record what these "commandments, statues and laws were," it seems unlikely that Esau would have been obedient to them:

When Esau was forty years old he married Judith the daughter of Beeri the Hittite, and Basemath the daughter of Elon the Hittite; and they brought grief to Isaac and Rebekah. (Gen 26:34-35)

Now Esau saw that Isaac had blessed Jacob and sent him away to Paddan-aram to take to himself a wife from there, and that when he blessed him he commanded him, saying, "You shall not take a wife from the daughters of Canaan," and that Jacob had obeyed his father and his mother and had gone to Paddan-aram. So Esau saw that the daughters of Canaan displeased his father Isaac; and Esau went to Ishmael, and married, besides the wives that he had, Mahalath the daughter of Ishmael, Abraham's son, the sister of Nebaioth. (Gen 28:6-9)

Sin, often understood as disobeying God's word, occurs much earlier than the actual commission or behavior. As Jesus explains His parable (Matt 15:10-11; Mark 7:14-15), He teaches the disciples that the outward sinful behavior of a person reflects the evil condition of the heart which is the real cause of defilement of a person.

Peter said to Him, "Explain the parable to us." Jesus said, "Are you also still lacking in understanding? Do you not understand that everything that goes into the mouth passes into the stomach, and is eliminated? But the things that come out of the mouth come from the heart, and those things defile the person. For out of the heart come evil thoughts, murders, acts of adultery, other immoral sexual acts, thefts, false testimonies, and slanderous statements. These are the things that defile the person; but to eat with unwashed hands does not defile the person." (Matt 15:15-20)

And when He later entered a house, away from the crowd, His disciples asked Him about the parable. And He said to them, "Are you so lacking in understanding as well? Do you not understand that whatever goes into the person from outside cannot defile him, because it does not go into his heart, but into his stomach, and is eliminated?" (Thereby He declared all foods clean.) And He was saying, "That which comes out of the person, that is what defiles the person. For from within, out of the hearts of people, come the evil thoughts, acts of sexual immorality, thefts, murders, acts of adultery, deeds of greed, wickedness, deceit, indecent behavior, envy, slander, pride, and foolishness. All these evil things come from within and defile the person." (Mark 7:17-22)

According to the author of James, the process of committing sin begins with a person's own desire, and then fulfilling it when tempted to do so. This forms the basis of understanding the cause of the seven behaviors that God hates (Prov 6:16-19).

But each one is tempted when he is carried away and enticed by his own lust. Then when lust has conceived, it gives birth to sin; and when sin is accomplished, it brings forth death. (Jam 1:14-15)

The idea that sin originates with one's desires was introduced by Jesus, "You have heard that it was said, 'You shall not commit adultery'; but I say to you that everyone who looks at a woman with lust for her has already committed adultery with her in his heart." (Matt 5:27-28)

This correlates very well with the Jesus' Greatest Commandment of desiring God:

And He said to him, "'You shall love the Lord your God with all your heart, and with all your soul, and with all your mind.' This is the great and foremost commandment." (Matt 22:37-38)

Throughout the Bible, as the seat of mankind's deepest convictions, beliefs and volitional will, it is the heart that is recognized as the root of mankind's problem. As representing the essence of a man, the heart is the primary focus of God's commands, calling and home for the Holy Spirit.

Then the LORD saw that the wickedness of man was great on the earth, and that every intent of the thoughts of his heart was only evil continually. (Gen 6:5)

"The heart is more deceitful than all else
And is desperately sick;
Who can understand it?
I, the Lord, search the heart,
I test the mind,
To give to each person according to his ways,
According to the results of his deeds." (Jer 17:9-10)

But the LORD said to Samuel, "Do not look at his appearance or at the height of his stature, because I have rejected him; for God does not see as man sees, since man looks at the outward appearance, but the LORD looks at the heart." (1 Sam 16:7)

Blessed are the pure in heart, for they shall see God. (Matt 5:8)

that if you confess with your mouth Jesus as Lord, and believe in your heart that God raised Him from the dead, you will be saved; for with the heart a person believes, resulting in righteousness, and with the mouth he confesses, resulting in salvation. (Rom 10:9-10)

who also sealed us and gave us the Spirit in our hearts as a pledge. (2 Cor 1:22)

Moreover the LORD your God will circumcise your heart and the heart of your descendants, to love the LORD your God with all your heart and with all your soul, so that you may live. (Deut 30:6)

God knew the condition of Esau's heart before he was born and that he would despise his birthright in the future, in essence despising the One who gave the birthrightwhich is why God hated Esau. With that knowledge, Joseph was chosen for the purpose of carrying on the Abrahamic Covenant, and Rebekah was informed that the "the older will serve the younger" (Gen 25:23; Rom 9:11-13).

It is noteworthy to consider that God will give those who He knows will oppose Him in the future a role in His plan of salvation.

Pharaoh was used to establish the reality of God's existence and basis of faith (Ex 19:4-6).

Herod the Great was used to fulfill two Messianic prophecies that validated Jesus as the Christ and Son of God (Hos 11:1; Matt 2:13-15 | Matt 2:19-23)