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Praying in the Spirit is being led by the Spirit in how, when, and for whom to pray. "For as many as are led by the Spirit of God, they are the sons of God." (Romans 8:14) For example, you may sense a leading one day to pray for a missionary that you haven't seen in many years. Prayer lists are useful, but there are times the Holy Spirit may call you to stand in the gap for something that wasn't on your radar screen. 1 John 5:14-15 tells us that effectual prayer agrees with God's will. His Word is His will. We can pray according to God's will using His Word. However, some things are mysteries to us. For example, the Bible says, "Beloved, I wish above all things that thou mayest prosper and be in health, even as thy soul prospereth." (3Jn 2). The Bible doesn't tell you where to get a job, invest, or what business to start. It also says,"Whoso findeth a wife findeth a good thing, and obtaineth favour of the Lord."(Pr 18:22) But how do you know WHERE to find her? Some things are mysteries. Praying in the Spirit allows us to pray about those mysteries. 1 Cor. 14:2 defines praying in the Spirit: "For he that speaketh in an unknown tongue speaketh not unto men, but unto God: for no man understandeth him; howbeit in the spirit he speaketh mysteries." Praying in the Spirit is allowing the Holy Spirit to lead you in prayer; it is also praying in tongues. I Cor 14:2 states that it does not have to be understood by man. What about 1 Cor. 14:27- If any man speak in an unknown tongue, let it be by two, or at the most by three, and that by course; and let one interpret. It seems as if 1 Corinthians 14:2 and 1 Corinthians 14:27 are incongruent. Some of the confusion about praying in the Spirit comes from not understanding that there are different manifestations of tongues that function in different ways for different purposes. There are diversities of gifts (1 Cor 12:4); And there are diversities of operations, but it is the same God which worketh all in all. (1 Cor 12:6) Tongues and interpretation are one manifestation of tongues; they function together to reveal the thoughts of God, usually to a group of people, as in a church service. Tongues as a sign to unbelievers is another manifestation is recorded in the second chapter of Acts. Therefore, you can see that 1 Corinthians 14:27 does not apply to every manifestation of tongues; there were no interpreters on the day of Pentecost, and you don’t need an interpreter to speak to God. Praying in tongues is a way for individuals to pray about things that the Holy Spirit knows (which is everything), but which are unknown to the person who prays. When you pray, you aren’t talking to people; you are speaking to God. Our prayer life is rendered ineffective when we don’t know how to pray. When someone asks for prayer, all you know is what that individual has revealed. The Holy Spirit knows the situation thoroughly. That is why Romans 8:26-27 tells us, Likewise the Spirit also helpeth our infirmities: for we know not what we should pray for as we ought: but the Spirit itself maketh intercession for us with groanings which cannot be uttered. And he that searcheth the hearts knoweth what is the mind of the Spirit, because he maketh intercession for the saints according to the will of God. In 1 Corinthians 2:13-14, the Apostle Paul acknowledged that praying in tongues is of the Spirit, and that doesn’t make sense to those who operate strictly from the mental realm: "Which things also we speak, not in the words which man's wisdom teacheth, but which the Holy Ghost teacheth; comparing spiritual things with spiritual. But the natural man receiveth not the things of the Spirit of God: for they are foolishness unto him: neither can he know them, because they are spiritually discerned." Praying in the Spirit is not necessary for salvation, but helps us to pray God's perfect will: "Thy will be done." (Matthew 6:10)
I like the late Warren Wiersbe's comments about praying in the Spirit. The Bible formula is that we pray to the Father, through the Son, and in the Spirit. Romans 8:26-27 tells us that only in the Spirit’s power can we pray in the will of God. Otherwise, our praying could be selfish and out of the will of God. In the Old Testament tabernacle, there was a small golden altar standing before the veil, and here the priest burned the incense (Ex. 30:1–10; Luke 1:1–11). The incense is a picture of prayer. It had to be mixed according to God’s plan and could not be counterfeited by man. The fire on the altar is a picture of the Holy Spirit, for it is He who takes our prayers and “ignites” them in the will of God. It is possible to pray fervently in the flesh and never get through to God. It is also possible to pray quietly in the Spirit and see God’s hand do great things. “Pray in the Holy Spirit” is contrasted with Jude 19— “having not the Spirit.”) It means to pray according to the leading of the Spirit. It has well been said by Robert Law, “Prayer is not getting man’s will done in heaven—it is getting God’s will done on earth.” This agrees with 1 John 5:14–15. As Christians, we may pray in solitude (Matt. 6:6), but we never pray alone; the Spirit of God joins with us as we pray (Rom. 8:26-28) because He knows the mind of God and can direct us. He can give us wisdom and knowledge from the Word (Eph. 1:15ff.). He can also help us approach the Father through the access we have in Jesus Christ (Eph. 2:18). We worship God “in the Spirit” (Phil. 3:3), and the Spirit motivates us to pray, for He is “the Spirit of grace and of supplications” (Zech. 12:10). When the believer is yielded to the Spirit, then the Spirit will assist him in his prayer life, and God will answer prayer.
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