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There is indeed much evidence that silent prayer was taught and practiced in the early church. Several examples from the first few centuries will demonstrate this:
Clement of Alexandria (150–215) writes:
Prayer is, then, to speak more boldly, converse with God. Though whispering, consequently, and not opening the lips, we speak in silence, yet we cry inwardly. For God hears continually all the inward converse. (Stromata, 7.7)
Cyprian (200–258) writes regarding Hannah:
she prayed to God not with clamorous petition, but silently and modestly, within the very recesses of her heart. She spoke with hidden prayer, but with manifest faith. She spoke not with her voice, but with her heart, because she knew that thus God hears; and she effectually obtained what she sought, because she asked it with belief. (Lord's Prayer, 5)
As far as the prevalence of the practice, this is a bit more difficult to confirm, but we do know that Cyril of Jerusalem (313–386) commanded it of women in his catechetical lectures:
let the married woman also [...] pray; and let her lips move, but her voice be unheard
It's also specifically commanded in the canons of the Council of Laodicea (363):
After the sermons of the Bishops [...] there should then be offered the three prayers of the faithful, the first to be said entirely in silence, the second and third aloud
Similarly, in the Apostolic Constitutions (380), Book 2, Section 7:
After this let the sacrifice follow, the people standing, and praying silently
It's tough to demonstrate exactly how common the practice was among individual Christians in the early church, given the documentary record that has survived. But the record clearly shows, particularly the last two documents cited above, that silent prayer was widespread in Christian churches by the 4th century, if not earlier.
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I'm wondering if you are specifically asking about silent prayer (reciting known prayers, asking God for blessings, praying for people, exalting God in silence) or if you are asking about contemplative prayer, which might appear on the outside more like meditation? It differs (in my opinion) in that you are calming your inner world, physically and mentally, to reach a still state where you can hear God speaking to you. Where He can impart onto you thoughts, insight, healing, direction, etc. that is beyond your current knowing. I have done it in a group where we focus on a specific passage from the Bible or alone, letting God lead me. As far as historical examples, I'm sure there are more than we know, but I am currently reading about St. Teresa of Avila who received this gift,from God,in the sixteenth century. I apologize if this is not what you were asking, but it was such an enlightening moment in my prayer life and journey, I could not stay silent on the off chance this is what you were looking for.
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What is the history of silent prayer?
Let us start with the words of our Lord in this matter first.
"And when you pray, do not be like the hypocrites, for they love to pray standing in the synagogues and on the street corners to be seen by men. I tell you the truth, they have received their reward in full. But when you pray, go into your room, close the door and pray to your Father, who is unseen. Then your Father, who sees what is done in secret, will reward you. And when you pray, do not keep on babbling like pagans, for they think they will be heard because of their many words. Do not be like them, for your Father knows what you need before you ask him.
"This, then, is how you should pray: "`Our Father in heaven, hallowed be your name, your kingdom come, your will be done on earth as it is in heaven. Give us today our daily bread. Forgive us our debts, as we also have forgiven our debtors. And lead us not into temptation, but deliver us from the evil one. Matthew 6:5-13
The Bible gives an example of silent prayer in Hannah’s inaudible petition (1 Samuel 1:10, 13), but it does not give specific instructions on praying silently. That does not mean that silent prayer is any less valid than praying out loud—Hannah’s prayer was answered, after all. God can hear our thoughts just as easily as He can hear our words (Psalm 139:23; Jeremiah 12:3). Jesus knew the evil thoughts of the Pharisees (Matthew 12:24-26; Luke 11:17). Nothing we do, say, or think is hidden from God, who does not need to hear our words to know our thoughts. He has access to all prayers directed to Him, whether or not they are spoken.
The Bible mentions praying in private (Matthew 6:6). What is the difference between praying aloud or silently if you are by yourself? There are some circumstances where only silent prayer is appropriate, e.g., praying for something that needs to stay between you and God only, praying for someone who is present, etc. There is not anything wrong with praying silently, as long as you are not doing it because you are embarrassed to be heard praying.
Perhaps the best verse to indicate the validity of unspoken prayers is 1 Thessalonians 5:17: “Pray without ceasing.” To pray unceasingly obviously cannot mean we are praying out loud all of the time. Rather, it means we are to be in a constant state of God-consciousness, where we take every thought captive to Him (2 Corinthians 10:5) and bring every situation, plan, fear, or concern before His throne. Unceasing prayer will include prayers that are spoken, whispered, shouted, sung, and silent as we direct our thoughts of praise, petition, supplication, and thanksgiving to God.
Praying silently has been a part of tradition since day one within Christianity. In modern times, it is more pronounced within more traditional denominations like Orthodoxy and Catholicism. Nevertheless, they are some denominations that almost prefer exclusively praying in silence such as Quakers.
Silent worship and the spoken word are both parts of Quaker ministry. The ministry of silence demands the faithful activity of every member in the meeting. As, together, we enter the depths of a living silence, the stillness of God, we find one another in ‘the things that are eternal’, upholding and strengthening one another. - Approaches to God – worship and prayer
It is also more commonly practiced outside of regulated liturgical functions such as at Eucharistic celebrations.
The Early Church greatly favoured silent prayer.
Compel yourselves in silence, the mother of all godly virtues. Keep silent, in order to say the Prayer [of Jesus]; for, when someone speaks, how is he able to escape idle talk, from which comes every evil word, which weighs the soul down by the responsibility for it. - Elder Ephraim of Philotheou Mount Athos
A characteristic of those who are still progressing in blessed mourning is temperance and silence of the lips; and of those who have made progress – freedom from anger and patient endurance of injuries; and of the perfect – humility, thirst for dishonors, voluntary craving for involuntary afflictions, non-condemnation of sinners, compassion even beyond one’s strength. The first are acceptable, the second laudable; but blessed are those who hunger for hardship and thirst for dishonor, for they shall be filled with the food whereof there can be no satiety. - St. John Climacus
For God is silence, and in silence is He sung by means of that psalmody which is worthy of Him. I am not speaking of the silence of the tongue, for if someone merely keeps his tongue silent, without knowing how to sing in mind and spirit, then he is simply unoccupied and becomes filled with evil thoughts: ... There is a silence of the tongue, there is a silence of the whole body, there is a silence of the soul, there is the silence of the mind, and there is the silence of the spirit. - John the Solitary
Intelligent silence is the mother of prayer, a recall from captivity, preservation of fire, an overseer of thoughts, a watch against enemies, a prison of mourning, a friend of tears, effective remembrance of death, a depicter of punishment, a delver into judgment, a minister of sorrow, an enemy of freedom of speech, a companion of stillness, an opponent of desire to teach, increase of knowledge, a creator of divine vision, unseen progress, secret ascent. - St. John Climacus
Gleanings from Orthodox Christian Authors and the Holy Fathers
One just has to read the lives of the Desert Father or founders of early monasticism to see how important silent prayer was regarded in antiquity. Such well known Desert Fathers such as Paul of Thebes, Anthony the Great, Arsenius the Great, Poemen, Macarius of Egypt, Moses the Black, and Syncletica of Alexandria, Pachomius and Shenouda the Archimandrite, and many individuals who spent part of their lives in the Egyptian desert, including Athanasius of Alexandria, John Chrysostom, Evagrius Ponticus, Hilarion and John Cassian.
It is obvious that members of the Early Church practiced silent prayer, and lead by the Holy Spirit were inspired to live lives dedicated to prayer as hermits and ascetics.
Hesychasm is a mystical tradition and movement that originated with the Desert Fathers and was central to their practice of prayer. Hesychasm for the Desert Fathers was primarily the practice of "interior silence and continual prayer." It did not become a formal movement of specific practices until the fourteenth century Byzantine meditative prayer techniques, when it was more closely identified with the Prayer of the Heart, or "Jesus Prayer". That prayer's origin is also traced back to the Desert Fathers—the Prayer of the Heart was found inscribed in the ruins of a cell from that period in the Egyptian desert. The earliest written reference to the practice of the Prayer of the Heart may be in a discourse collected in the Philokalia on Abba Philimon, a Desert Father. Hesychast prayer was a meditative practice that was traditionally done in silence and with eyes closed—"empty of mental pictures" and visual concepts, but with the intense consciousness of God's presence.
The words hesychast and hesychia were frequently used in 4th and 5th century writings of Desert Fathers such as Macarius of Egypt, Evagrius Ponticus, and Gregory of Nyssa. The title hesychast was used in early times synonymously with hermit, as compared to a cenobite who lived in community. Hesychasm can refer to inner or outer stillness, though in The Sayings of the Desert Fathers it referred to inner tranquility. - Desert Fathers
Christian mystics, from within Orthodoxy and Catholicism place a great importance into the use of silent prayer. Within Catholicism it is generally referred to as contemplative prayer or mental prayer.
Catholic Mental Prayer, also called Catholic meditation, is a form of silent prayer that is the next level advanced from vocal prayer.
All the saints practiced it. St. Alphonsus Liguori said: "every saint became a saint through Mental Prayer."
Benefits of Mental Prayer In every meditation, we are examining ourselves to see how we are following Christ: are we being humble? have we grown lukewarm?
Thus meditation provides a way of conquering our vices, especially our predominant ones, growing in virtue, remaining closer to God throughout the day, and sprinting along the track to sainthood that our Lord has prepared for us.
One cannot become as holy as God wills without meditation. The saints all meditated (and ascended to higher levels of prayer).
One cannot conquer venial sin without meditation, a claim I had never heard before!
Meditation is the gateway to deeper forms of prayer, but you can’t bypass it.
Years ago I read books by St. John of the Cross and St. Teresa of Avila–two saints considered geniuses on prayer–but it was too deep for me. I couldn’t understand, practically, how to meditate and begin to penetrate into the inner levels of the Interior Castle.