Have the verses of the Holy Quran been compiled and gathered according to the taste, liking and desire of the companions or according to the will and instruction of the Holy Prophet, peace be upon him. Did Uthman not put the Quranic verses relating to caliphate and vicegerency among the verses of Ahkaam (legal rules)? Is publication of the Quran on the basis of the sequence of the revelation a kind of innovation (bid’ah)? If it is not, why does the Islamic Republic of Iran not print and publish the Quran on the basis of the order of the revelation? Given the outburst of information and minimization of ignorance in religious issues, isn’t it high time that the Islamic Republic of Iran left aside the predecessors’ considerations and took a bold action to overwhelm, with reliance on the chronology of revelation, contexts and evidence, the performance of the tyrant and repressive companions by publishing and presenting a new Mushaf (scripture) that would match the Quran that was revealed to the Holy Prophet (s)?..
According to the history of the compilation of the Quran, the Prophet (s) himself chose the verses where to be placed. It was not the companions who arranged the verses or the number of the chapters. The Quran, which is presently in our hands and which is available to every Muslim, is the same Quran which was collected and compiled during the period of Uthman. Given that a group of reciters and memorizers of the Holy Quran were cooperating in the compilation of the Quran, we cannot say that the Quranic verses were arranged by the order and according to the liking and desire of Uthman. In addition, there are many traditions from the infallible Imams (a.s.) which denote that they sanctioned and approved the compilation of the verses during Uthman’s era.
The compilation of the Holy Qur’an took place in three stages:
1. Arrangement of verses which led to formation of the chapters. This was done during the period of the Holy Prophet (s). It was the Prophet himself who would indicate in which Surahs each verse was to be placed.
2. Collections of the Quran and separate pages (or parchments) and putting them together in the form of a single volume. This was done during during the period of Abu Bakr.
3. Collection of different copies of the Quran which had been written down by scribes and making them look the same in order to prevent variation in the copies. This was done during the period of Uthman, the third caliph.
There is ample evidence showing that the entire Qur’an was written down in the Prophets (s) lifetime. Based on historical reports, when he (s) received revelation he would instruct scribes to record the revelation on parchments of paper or pieces of leather. He would also indicate in which Surah each ayah was to be placed. The Companions never interfered in the arrangement of the ayahs and Surahs which are the same in copies of Qurans available today.
Following the demise of the Holy Prophet (s), the compilation of the Holy Quran took place by the order of the first caliph with the help of Zaid bin Thabit. Before him also, the Commander of the Faithful, Ali (a.s.) who was more acquainted with the Quran than all other Companions had compiled the Quran. Indeed, in the wake of the Islamic conquests and the growing trend to convert to Islam in the second and third Islamic centuries, there were more and more people to write the Quran and make copies of it. Every individual who had the ability to write embarked on writing the Quran from the famous copies available to them. There are some reports in the historical sources which indicate that there were discrepancies among Muslims concerning the recitation of the Quran. These discrepancies led some Muslims to look for some solution.
The suggestion to make standard reference of the Holy Quran was put forth by Hudaifah to Uthman. The latter called on the Companions who all agreed to the proposal and promised to cooperated in this regard. Uthman then chose a committee of four people: Zayd ibn Thabit, 'Abdullah ibn az-Zubayr, Sa'id ibn al-'As and 'Abd al-Qays to carry out designated task. Later on more people joined them and their number reached up to twelve. Uthman commanded them to write the Quran in the language of Quraish because it had been revealed in that language.
The standard reference team was established in the year 25 of Hegira year, and the first action taken by them by the order of Uthman was to collect the various copies of the Quran from all parts of the expansive Islamic country.
At this stage, different and various copies of the Quran were collected and sent to Medina and they were burnt or dumped into boiling water at the behest of the third caliph. For this reason, Uthman was also called Harraq al-Masahef [Burner of Scriptures]. The last stage involved sending newly written standard copies of the Quran out to other cities along with a reciter to recite the Quran with correct pronunciation to people. This was also done by the third caliph. 
Historians are not unanimous about the number of the copies of the Quran provided and sent out to different parts of the Islamic country. Ibn Abi Dawood says that there were six copies of the Quran sent to Makkah, Kufa, Basra, Syria, Bahrain and Yemen. One copy of the Book which was called Umm (mother) or Imam (master) was kept in Medina. Another historian named Ya’qubi adds another two volumes to it saying that one copy of the Quran was sent to Egypt and another to Al-Jazirah. The copies which were sent to various regions were kept therein and they were used as standard references to make more and more copies available to people using them.
The sequence and order of Uthman’s scripture was the same order that exist with the present available copy of the Quran. It matched with the order that had been applied to scriptures of the companions especially Ubai bin Ka’b. It should be noted that during the early period of Islam and in the time of the caliphs, the Quran manuscripts had no sign of punctuation because using punctuations was not common at that time.
Shiites agree unanimously that the Quran which is available in every Muslim’s house is the same complete Quran and Uthman’s scripture (mushaf) is that which is in our hand; it is free from any alterations or distortions. Although the Quran which had been compiled by Imam Ali (a.s) was arranged on the basis of the order of the revelation of the chapters, since the present Quran has been approved and sanctioned by the Infallible Imams (a.s.), there is no need to print the Quran on the basis of the order of revelation, even if it may not be bid’ah (innovation); because bi’ah means adding to the religion what is not a part of it. Bid’ah in this sense is forbidden as also stated by the Imams, peace be upon them.
A man who was in the company of Imam Sadiq, peace be upon him, recited a letter from the Quranic verse differently from what people used to recite normally. The Imam hearing that said: “Do not recite this letter in that way; recite it in the way other people recite it.”
The Commander of the Faithful, Ali (a.s.) expressed his consent somehow with unification of the scriptures. Ibn-e Abi Dawood narrates from Suwaid bin Ghaflah that Ali, peace be upon him, said: “By Allah, Uthman did not do anything about Mushaf except after seeking my advice.”
In another narration, Imam Ali (a.s) has been narrated as having said: “If I were in command in place of Uthman, I would have done the same".
The concluding point to mention here is that according to the history of the compilation of the Quran, the Prophet (s) himself chose the verses where to be placed. It was not the companions who arranged the verses or the number of the chapters. The Quran, which is presently in our hands and which is available to every Muslim, is the same Quran which was collected and compiled during the period of Uthman. Given that a group of reciters and memorizers of the Holy Quran were cooperating in the compilation of the Quran, we cannot say that the Quranic verses were arranged by the order and according to the liking and desire of Uthman. In addition, there are many traditions from the infallible Imams (a.s.) which denote that they sanctioned and approved the compilation of the verses during Uthman’s era.
 - Lessons from the Quran, Hussein, Jawan Arasteh, pg. 198, Islamic Propagations Office Publications, Qom, 3rd edition, 1378 (1999).
 - Ibid, 203.
 - Amuzesh Uloom Quran, translation of Al-Tamhid fi Uloom al-Quran, Muhammad Hadi Ma’arefat, translated by Abu Muhammad Wakili, vol.1, pg. 425, Islamic Propagations Organizations Printing and Publication House, Qom, 1st edition, 1371 (1992).