There is no recommendation from the Holy Prophet, peace be upon him and his family, about the arrangement of the text of the Quran on the basis of the chronological order of revelation. The Holy Quran was compiled in several stages. Imam Ali, peace be upon him, compiled the Quran on the basis of the chronological order of revelation but finally the compilation rendered by the caliphs became public and the Ahlul-Bayt (A.S.) also completely certified the present compilation.
There are three opinions regarding the collection and compilation of the Quran:
1. The verses of every chapter (Sura) were revealed completely and until a chapter was not completed, another chapter would not start.
2. Several verses were revealed from every chapter and the chapters were completed gradually. The question which arises here is: Were the verses placed in different chapters of the Quran by the order of the Holy Prophet (S) or was this arrangement made during the time of the Companions?
3. The order of the verses and that of the chapters of the Quran has been decided during the period of the Companions.
A Study of the First View:
Suyuti has mentioned a narration in his ‘Al-Etqan’ which shows that the Prophet and Muslims understand through “Bismillahir Rahman al-Rahim” (In the Name of God, the Compassionate the Merciful) that the previous Sura has ended and a new one has started. This report implies that every chapter would be revealed completely in the time of the Prophet (S). However, since Muslim scholars agree that during the early period of the prophetic mission, only a few verses of Chapter al-Alaq (not the complete Chapter) were revealed and when the verses were revealed, the Prophet (S) would place them in their appropriate chapters, this supposition is not reliable.
A Study of the Second View:
As was stated in the first section, several verses named in history were instructed by the Prophet (S) to be placed in various chapters of the Holy Quran. The Quran was first compiled by Abu Bakr, then by Uthman with no verses moved from their places. Basically, the two caliphs had nothing to do with the arrangement of the verses. Although some chapters like “Fatihat-ul Kitab” (the beginning chapter of the Book) was revealed completely, some other chapters especially the lengthy ones were revealed overtime and sometimes simultaneously with other verses. That is to say, some verses from every chapter were revealed and completed gradually.
In this regard, late Tabarsi, the author of Tafsir Majma’ul Bayan, says: “When it comes to the sequence of the revelation, the sequence of every chapter is observed with the revelation of the beginning of every chapter. Hence, if a few verses of a chapter are revealed and before it is completed, verses from other chapters are sent down and it may happen that many chapters may be revealed completely, then the remaining verses of the first chapter are revealed in which case the sequence of the verses (their being Makki or Madani) depends on the revelation of the beginning of every verse.”
The arrangement of the verses in different Quranic chapters was done as instructed by the Prophet (S) but different copies of the Holy Quran were collected during the period of Uthman and no copy would be accepted unless it was certified by at least 2 witnesses. The witnesses would have to have seen it being written down, not from memory, but at the very dictation of the prophet (S).
A Study of the Third View:
Muslim scholars almost agree that the present arrangement of the verses was made by the Prophet himself, and thus the arrangement of every verse in the Qur'an is tawqifi (i.e. something that has come to us from Almighty Allah) but the order of the chapters as was mentioned above was decided during the time of the Companions. In fact, there are some narrations which indicate that the Quran was collected also during the Prophet (S) and if we accept this saying (which is strong per se), then the conclusion we can draw out is that the Quran has been collected in three stages i.e. in the time of the Prophet (S), the first and second caliphs and finally the third caliph.
Collection of the Holy Quran:
The Quran was collected by some Companions at the behest of the Prophet, peace be upon him and his family. This collection was in fact nothing but the inscription of the revelation. During the time of Abu Bakr, the first caliph, different parchments and the scattered verses were collected between two covers (in a single collection like the present Book). Finally, during the period of Uthman in which different copies of the Quran had been spread far and wide and it was recited in different ways, the different copies were collected and a standard copy was created out of all of them.
Mus’haf of Imam Ali (A.S.)
What is meant by the Mus’haf of Imam Ali (A.S.) is the Quran which he compiled after the passing of the prophet (S). In this Quran things like the exact chronological order of the verses and chapters according to the time of their revelation have been mentioned, all in compliance with the original recitation of the Prophet (S) himself. The Makki verses precede the Madani ones. However, this Quran was not accepted by some of the Companions who claimed the caliphate. Finally, the present Quran which was last collected and compiled by Uthman, the third caliph, was certified by Imam Ali, peace be upon him.
Conclusion: Having said the above, it can be concluded that:
1 – The verses of the Quran, in its gradual revelation, were sometimes sent down in the form of a complete chapter and other times in the form of a few verses from a chapter.
2 – Sometimes verses were revealed from another chapter before completion of the first chapter.
3 – There were some Sahabis (Companions) who compiled the Quran by the order of the Prophet and according to his arrangement, not on the basis of the order of revelation.
4 – The arrangement of every verse in the Qur'an is tawqifi (i.e. something that has come to us from Almighty Allah).
5 – The arrangement of the chapters, as per a saying, was made during the time of the Companions especially Uthman.
6 – The collection of the Quran during the time of the Holy Prophet (S) was in fact the inscription of the revealed verses. During the time of the first and second caliphs, different parchments and the scattered verses were collected and made available in a single collection. Finally, the collection of the Quran during the period of the third caliph helped do away with different recitations that had come into being over the years.
7 – Imam Ali (a.s.) compiled the Quran on the basis of the chronological order of the Quran. However, since the present Quran which was compiled by Uthman was acceptable to him, he certified it and did not make his compiled version of the Quran public.
 -Ibn Abbas has said: “The Apostle of God, (S) did not know when a chapter would end until “Bismillahir Rahman al-Rahim” was revealed. Bazzar has added that when “Bismillahir Rahman al-Rahim” was revealed, then everybody would know that one chapter has ended and another has started. Tafsir al-Mizan, vol.12, pg. 186.
 - Ma’refat, Muhammad Hadi, Uloom Qurani (Quranic Sciences), pg. 76, Al-Tamhid Institute, Qom, 1378.
 - Ibid, pg. 77; Ibn Ashur, Al-Tahrir wat-Tanvir, vol.1, pg.90. Al-Tirmidhi narrates from Ibn Abbas, he from Uthman that he said: When the verses of the Qur'an were revealed to the Prophet (peace be upon him and his progeny), he called someone to write them down for him and said to him: Put this verse in the surah in which such and such has been mentioned; and when one or two verses were revealed, he used to say similarly (regarding them).”
 - Uloom Quran (Quranic Sciences), pg. 76
 - Tabarsi, Fadhl bin al-Hasan, Majma’ul Bayan fi Tafsir al-Quran, translation of translators, vol.26, pg. 147, Farahani Publications, Tehran, 1360, with some modifications and deductions; Uloom Quran (Quranic Sciences), pg. 89.
 - Translation of Al-Mizan, vol.12, pg. 174.
 - Although this an agreed-upon view, there are some Shia exegetes like Muhammad bin Habibullah Sabzevari Najafi who has opposed this in his “al-Jadid fi Tafsir al-Quran al-Majid”, vol.2, pg. 420. Similarly, there are some non-Shia scholars like Shawkani who has oppose this view in his “Fathul Qadir”, vol.1, pg. 86.
 - Suyuti, Al-Etqan, fi Uloom al-Quran, vol.1, pg. 71; Uloom Quran (Quranic Sciences), pg. 119.
 - Al-Etqan, fi Uloom al-Quran, vol.1, pg.69; Bukhari, Muhammad bin Ismail, Sahih al-Bukhari, vol.4, pg. 1907, Dar ibn Kathir, Beirut, 1407.
 - Ali bin Sulayman al-Ubaid, Jam’ al-Quran Hifdhan wa Kitabatan, pg. 70, Al-Matlab al-Awwal, al-Adillah alaa kitabat al-Quran al-Karim fi Ahdehi sallallahu alayhi wa sallam, in which al-Bukhari and Muslim narrate from Ibn Umar that “The Messenger of Allah forbade a Muslim to travel to enemy territory with the Quran.” Muslim says that the Messenger of Allah (peace be upon him) said: Do not travel with the Quran because I fear lest the Quran should fall in the hand of the enemy.”
 - Maghrizi, Ahmad bin Ali, Amta’ul Asma’, vol.4, pg.239, Dar al-Kutub al-Ilmiyah, Beirut, 1420.
 - See: Jam’ al-Quran Hifdhan wa Kitabatan, pg. 70 (about the collection of the Quran in the time of the Prophet); Al-Etqan, vol.1, pg. 67 and 69 (about the collection of the Quran during Abu Bakr and Uthman).
 - As was stated, some of the verses of the Quran were placed in special chapters as instructed by the Prophet (S).
 - In the terminology of the commentators, a Makki verse was revealed before Hijrah (migration) to Madinah, and a Madani verse was revealed after.
 - Uloom Qurani, pg. 121, Muhammad bin Sa’d, Al-Tabaqat al-Kubra, Translated by Mahdawi Damghani, vol.2, pg. 324, Farhang wa Andisha Publications, Tehran, 1374 (1995).
 - Uloom Quran (Quranic Sciences), pg. 122.
 - When Ali (A.S.) arrived in Kufa [during his caliphate], a man stood up and denounced Uthman for having made people to read and adhere to one and the same copy of the Quran. Imam Ali (a.s.) shouted, “Be silent! Whatever he did, he did it after consulting me and getting my consent. If I were in command in place of him, I would have done the same." See: A’tham ibn Kufi, Al-Fotuh, translated by Mustawfi Herawi, pg. 997, Islamic Revolution Education and Publication Institute, Tehran, 1372 (1993), Uloom Qurani, pg. 122 - 123.