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Psalm 99: Holy is He!

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There is probably no attribute of God which needs to be taught and recognized more in our day than His holiness. David Wells emphasized this in God in the Wasteland [Eerdmans, 1994], his analysis of how the modern culture has infected the church. He observes (p. 114),

We have turned to a God that we can use rather than to a God we must obey; we have turned to a God who will fulfill all our needs rather than to a God before whom we must surrender our rights to ourselves. He is a God for us, for our satisfaction—not because we have learned to think of him this way through Christ but because we have learned to think of him this way through the marketplace. In the marketplace, everything is for us, for our pleasure, for our satisfaction, and we have come to assume that it must be so in the church as well. And so we transform the God of mercy into a God who is at our mercy.

He goes on to argue that the modern church is infatuated with the love of God and embarrassed at his holiness. We are more enamored with the therapeutic and psychological “uses” of God to provide us with inner peace, than we are with the fact that He is holy and therefore, we must be holy. And if we do not revere God as holy, then He rests lightly on us. We take Him or leave Him to the degree that we find Him useful. Wells later writes (p. 136), “Holiness is what defines God’s character most fundamentally, and a vision of this holiness should inspire his people and evoke their worship, sustain their character, fuel their passion for truth, and encourage persistence in efforts to do his will and call on his name in petitionary prayer.”

Psalm 99 calls us reverently to worship God because He is holy. There is an obvious contrast with Psalm 97:1, “The Lord reigns, let the earth rejoice.” Here (Ps. 99:1) it is, “The Lord reigns, let the peoples tremble.” Derek Kidner (Psalms 73-150 [IVP], pp. 353-354) describes the difference between Psalms 98 (emphasizing joy and singing) and 99 as “between high festivity and a chastened awe—for God is all that stirs us and all that shames us. Here, after the carefree delight of Psalm 98, we recollect how exalted and holy He is, and how profound is the reverence we owe Him.”

Psalm 99 falls into three sections, the first two (1-3, 4-5) ending with the refrain, “Holy is He,” and the third (6-9) with, “Holy is the Lord our God.” This threefold repetition of God’s holiness reminds us of the angelic refrain in Isaiah’s vision of God (Isa. 6:3), “Holy, Holy, Holy, is the Lord of hosts, the whole earth is full of His glory.” In Isaiah, the foundations of the thresholds trembled; here (Ps. 99:1b), the earth shakes. In Isaiah, the temple filled with smoke. Here (99:7), God speaks to His servants out of the pillar of cloud. In Isaiah, the angel flew to him with a burning coal and touched his lips, assuring him that his sin was forgiven. Here (99:8), we are told that God forgives the sins of His people, but also is an avenger of their evil deeds.

The mood of Psalm 99 is one of reverence and yet intimacy: He is the Lord our God (5, 8, 9 [2 times]). And, the awesomeness and holiness of God implies that we must bow in submission and obedience before Him. So we can sum up the psalm by saying,

Because the Lord is holy, worship Him in reverent intimacy, with a submissive heart.

1. The Lord reigns in holiness—worship Him in reverence (99:1-3).

“The Lord reigns, let the peoples tremble; He is enthroned above the cherubim, let the earth shake! The Lord is great in Zion, and He is exalted above all the peoples. Let them praise Your great and awesome name; holy is He.”

A. The Lord reigns—worship Him in reverence.

We considered the meaning of “the Lord reigns” in our study of Psalm 97:1 last week, so I won’t belabor the point now. But we would be remiss to brush over it without any comment, because it has such profound implications. Adam Clarke (Clarke’s Commentary [Abingdon-Cokesbury Press], 3:528, italics his) comments,

Here is a simple proposition, which is a self-evident axiom, and requires no proof: Jehovah is infinite and eternal; is possessed of unlimited power and unerring wisdom; as he is the Maker, so he must be the Governor, of all things. His authority is absolute, and his government therefore universal. In all places, on all occasions, and in all times, Jehovah reigns.

Even though the Lord, for His own inscrutable purposes, has allowed fallen angels and sinful people to rebel against Him, He still reigns over them, and yet is in no way stained by their sin. The Bible promises that the day is coming when Satan and his forces and all that have followed him will be cast into the lake of fire forever and ever. God’s saints will then be in a state of eternal sinlessness. Then, as John heard the voices from heaven proclaim (Rev. 11:15), “The kingdom of the world has become the kingdom of our Lord and of His Christ; and He will reign forever and ever.”

Or, again John heard the voices of a great multitude in heaven proclaim (Rev. 19:6b-7), “Hallelujah! For the Lord our God, the Almighty, reigns. Let us rejoice and be glad and give the glory to Him, for the marriage of the Lamb has come and His bride has made herself ready.” Until that glorious day of consummation, we should take great comfort in the fact that “the Lord reigns.”

“The peoples” refers to the Gentiles. Their response to the fact that the Lord reigns should be, first fear and then praise. They should tremble as even the earth shakes at the Lord’s reign. As they recognize that the Lord is exalted over them, they should praise His great and awesome name (99:3).

The Lord is pictured as “enthroned above the cherubim” (99:1b; see also, 1 Sam. 4:4; 2 Sam. 6:2; 2 Kings 19:15; 1 Chron. 13:6; Ps. 80:1; Isa. 37:16). The cherubim are a rank of angelic beings. There are several debates concerning them, but everyone agrees that they are impressive creatures (Zondervan Pictorial Encyclopedia of the Bible, ed. by Merrill Tenney [Zondervan, 1975], 1:788-790). The picture here comes from the Ark of the Covenant. God instructed Moses to make a mercy seat of pure gold, with two cherubim at both ends, facing one another, with their wings covering the mercy seat. God told Moses that He would meet with him there, from above the mercy seat between the two cherubim (Exod. 25:17-22).

The only one who could enter the Holy of Holies without dying was the high priest, and he could only go in there on the annual Day of Atonement. The cloud of God’s shekinah glory would fill that sacred place. They tied a rope around the high priest so that if he died, they could drag him out of there without anyone else dying! So the picture of God being enthroned or sitting above the cherubim is primarily one of His awesome holiness. That’s why the earth should shake.

And yet at the same time, the picture of God enthroned above the cherubim was a picture of His mercy towards sinners. It was on the mercy seat that the high priest sprinkled the blood of atonement, securing forgiveness of the sins of the nation. This looked ahead to the blood of Jesus, God’s final sacrifice for sins (see Hebrews 9 & 10). And so these verses have a prophetic focus, pointing to the reign of the risen Lord Jesus, whose blood sprinkled God’s mercy seat to atone for sinners. His sovereign reign, coupled with His great mercy, should cause us to worship Him with holy reverence.

B. The Lord reigns in holiness—worship Him in reverence.

The first section ends, as the second and third do, by stating, “Holy is He.” This is a fundamental attribute of God that we need to understand. The word means, primarily, “to be separate.” Theologian Louis Berkhof (Systematic Theology [Eerdmans], p. 73, italics his) explains that in this sense,

[God] is absolutely distinct from all His creatures, and is exalted above them in infinite majesty. … It is quite evident, however, that holiness in this sense of the word is not really a moral attribute, which can be co-ordinated with the others, such as love, grace and mercy, but is rather something that is co-extensive with, and applicable to, everything that can be predicated of God. He is holy in everything that reveals Him, in His goodness and grace as well as in His justice and wrath.

But the holiness of God also refers to His absolute moral purity. He is completely without sin and apart from it. “God is light, and in Him there is no darkness at all” (1 John 1:5; see also, Job 34:10; Hab. 1:13). This moral purity is not only negative, but also positive, in that God is morally or ethically perfect (Berkhof, ibid.).

Stephen Charnock (The Existence and Attributes of God [Baker], 2:110) writes,

The holiness of God is his glory, as his grace is his riches: holiness is his crown, and his mercy is his treasure. This is the blessedness and nobleness of his nature; it renders him glorious in himself, and glorious to his creatures, that understand any thing of this lovely perfection.

He points out that God is called holy more often than any other title. Further (2:112), there is no other attribute of God repeated three times in the praise of it. We never read of the angels crying out, “Eternal, eternal, eternal,” or “Faithful, faithful, faithful,” or “Love, love, love.” Charnock adds (2:113), “Power is his hand and arm; omniscience, his eye; mercy, his bowels; eternity, his duration; his holiness is his beauty….” He points out (ibid.) how God’s holiness relates to all of His perfections:

His justice is a holy justice; his wisdom a holy wisdom; his arm of power a holy arm (Ps. 98:1); his truth or promise a holy promise (Ps. 105:42). Holy and true go hand in hand (Rev. 6:10). His name, which signifies all his attributes in conjunction, is holy (Ps. 103:1); yea, he is “righteous in all his ways, and holy in all his works: (Ps. 145:17): it is the rule of all his acts, the source of all his punishments.

If we get even a glimpse of God as holy, our only response can be to worship Him with reverence, examining ourselves to make sure that we are growing in personal holiness. Peter put it this way (1 Pet. 1:14-19),

As obedient children, do not be conformed to the former lusts which were yours in your ignorance, but like the Holy One who called you, be holy yourselves also in all your behavior; because it is written, “You shall be holy, for I am holy.” If you address as Father the One who impartially judges according to each one’s work, conduct yourselves in fear during the time of your stay on earth; knowing that you were not redeemed with perishable things like silver or gold from your futile way of life inherited from your forefathers, but with precious blood, as of a lamb unblemished and spotless, the blood of Christ.

Last year I read about a professor at a Christian college who mentioned the fear of God in his classroom and was stunned when all of his students argued with him that we should not fear God, because it is opposed to His love! But Peter says to conduct yourself in fear. Paul sums up his discourse on the depravity of the human race by saying (Rom. 3:18), “There is no fear of God before their eyes.” It is safe to say that if you do not fear God, you do not know Him. Knowing that He is holy should lead us to worship Him with reverent fear.

2. The Lord reigns in justice and righteousness—worship Him with a submissive heart (99:4-5).

“The strength of the King loves justice; You have established equity; You have executed justice and righteousness in Jacob. Exalt the Lord our God and worship at His footstool; holy is He.”

A strong king who lacks a passion for justice will be a tyrant, as we know well from history. God is strong, but He also loves justice. He rules with equity (fairness), justice, and righteousness. His power never runs amok, because it is perfectly balanced with His justice and righteousness. His omniscience means that He will always judge fairly, because He knows not only all outward circumstances, but also every motive of the hearts of those He judges. The psalmist’s use of “Jacob” in reference to the nation is a common designation, and so may not have any significance here. But as you know, Jacob was known as a deceiver and schemer. But by way of contrast, God has “executed justice and righteousness in Jacob.”

Knowing that one day we all will stand before the judgment seat of Christ to give an account of ourselves to God (Rom. 14:10-12; 2 Cor. 5:10) should motivate us to live to please Him. It is possible to go through the outward motions of “worship” without submitting our hearts to God (Mark 7:6-7). The antidote is to “exalt the Lord our God and worship at His footstool” (Ps. 99:5), recognizing that He is holy. His footstool refers to the Ark of the Covenant (1 Chron. 28:2), or by association, to the temple, where God dwelled among His people. But footstool pictures bowing before the throne of a monarch, in total submission to him. Because our King is the righteous Judge of all, we must submit our hearts completely to Him, so that we worship Him in sincerity and truth.

3. The Lord reigns in faithfulness, mercy, and righteousness—worship Him with reverent intimacy (99:6-9).

A. The Lord reigns in faithfulness, mercy, and righteousness (99:6-8).

“Moses and Aaron were among His priests, and Samuel was among those who called on His name; they called upon the Lord and He answered them. He spoke to them in the pillar of cloud; they kept His testimonies and the statute that He gave them. O Lord our God, You answered them; You were a forgiving God to them, and yet an avenger of their evil deeds.”

The psalmist rehearses the history of God’s dealings with Israel through three of their prominent leaders. Moses and Aaron led the nation out of Egypt and established national worship through the tabernacle. Samuel came later, as the last of Israel’s judges who anointed the first king, Saul, and later, David.

All three men had their faults, but they were men of prayer and faith. God’s speaking to them in the pillar of cloud refers only to Moses and Aaron, not to Samuel. But God answered the prayers of all three men (see 1 Sam. 7:5-11). Moses and Aaron stood in the gap and intervened more than once to save the rebellious nation from God’s wiping them out (Num. 16:41-50). Aaron notoriously failed in the incident with the golden calf. Moses failed by striking the rock, when God had told him to speak to it. Samuel failed in that his sons did not follow the Lord. So they were men of flesh, and yet they cried out to God and He graciously answered them, while at the same time inflicting consequences when they sinned. But overall it may be said that they “kept [the Lord’s] testimonies and the statute that He gave them” (99:7).

Many commentators understand the pronouns in verse 8 to extend beyond these men to the nation. In other words, through their intercession, God’s forgiveness extended to the nation, although the Lord still imposed penalties for national disobedience. But however you apply verse 8, it shows the balance between God’s faithfulness in answering prayer, His mercy in forgiving sin, and His righteousness in imposing punishment for sin, so that we do not take His mercy lightly. We must never sin with the thought that we can always expect grace and forgiveness. Our sin always has severe consequences in damaging people and in tarnishing the Lord’s glory. And yet when we have sinned, we can come to Him and plead for His mercy.

David’s sin with Bathsheba illustrates this as well as any story in the Bible. David appealed to God for forgiveness and mercy, and it was granted. And yet, while assuring David that God had forgiven his sin, Nathan the prophet spelled out the dire consequences that God would impose. David’s son conceived in adultery with Bathsheba would die. The sword would not depart from David’s house. God would raise up evil against David from his own house and even give David’s wives to his son Absalom, who would lie with them in broad daylight (2 Sam. 12:9-14). God was sovereign in ordaining these events, and yet Absalom and the others who would sin were responsible. God’s holiness is not compromised when He uses evil people to accomplish His sovereign purposes. He reigns in faithfulness, mercy, and righteousness. This should lead us to deeper worship:

B. Exalt the Lord and worship Him with reverent intimacy, because He is holy (99:9).

The psalmist repeats the refrain (99:3, 5) with some slight variations: “Exalt the Lord our God and worship at His holy hill, for holy is the Lord our God” (99:9). Instead of “worship at His footstool” (99:5), he says, “worship at His holy hill,” which refers to the temple mount. Instead of “holy is He,” he gives a more intimate appeal, “for holy is the Lord our God.” Derek Kidner (p. 355) puts it, “The majesty is undiminished, but the last word is now given to intimacy. He is holy; He is also, against all our deserving, not ashamed to be called ours. Well may we worship.”

Or, in the words of Hebrews 12:22-24, which contrast the experience of Israel at Mount Sinai with our privileges,

But you have come to Mount Zion and to the city of the living God, the heavenly Jerusalem, and to myriads of angels, to the general assembly and church of the firstborn who are enrolled in heaven, and to God, the Judge of all, and to the spirits of righteous men made perfect, and to Jesus, the mediator of a new covenant, and to the sprinkled blood, which speaks better than the blood of Abel.

Jumping to his bottom line (12:28-29), “Therefore, since we receive a kingdom which cannot be shaken, let us show gratitude, by which we may offer to God an acceptable service with reverence and awe, for our God is a consuming fire.”

We can worship God intimately through Jesus our Mediator, but always with reverence and awe.


Let me apply this message with four directives:

First, aim at getting a bigger view of God in His majesty and holiness. As you read the Bible, like Moses (Exod. 33:18), ask God to show you His glory. Moses had already seen God’s majesty and power at Mount Sinai. He had communed with God for forty days and nights on that mountain. He had repeatedly seen the Shekinah glory. Wasn’t that enough? No, Moses wanted to see more! In addition to the Bible, read authors who exalt God. No one has helped me more on this than John Calvin. If you prefer more modern authors, read Martyn Lloyd-Jones, John Piper, and R. C. Sproul, especially his The Holiness of God [Tyndale, 1985].

Second, aim at getting a more biblically accurate view of yourself in God’s holy presence. This will follow the first aim almost spontaneously, as it did with Isaiah. Seeing God in His majesty and holiness will cause you to see yourself as a needy recipient of His grace.

Third, aim at increasing personal holiness on the heart level. Judge and cut off every sinful thought the instant it pops into your mind. Don’t tolerate so-called little sins as if they don’t matter. Don’t justify yourself with the consolation that everyone does it. Don’t expose yourself to TV shows or movies that defile you. If you wouldn’t be comfortable watching it with the Lord, don’t watch it.

Fourth, aim at meeting alone with God every day to exalt Him and worship at His footstool. The point of your quiet time is not just to read through the Bible in a year, although that’s a good thing to do. The point is to meet with God. See Him as revealed in His Word. Humble your heart before Him. Call upon Him in prayer. And remember, “Holy is the Lord our God.”

Application Questions

  1. Where is the proper biblical balance between fearing God and being close to Him? How can we know the boundaries?
  2. If you applied the question, “Will this help me to grow in holiness?” how would your usual activities change?
  3. Should Christians fear God’s judgment? Consider 2 Corinthians 5:10-11 and Romans 14:10-12 in your answer.
  4. What has helped you most to grow in your understanding of God’s holiness? What goals could help you move in that direction this year?

Copyright, Steven J. Cole, 2009, All Rights Reserved.

Unless otherwise noted, all Scripture Quotations are from the New American Standard Bible, Updated Edition © The Lockman Foundation

Related Topics: Worship (Personal), Character of God

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