After researching on this topic, it is safe to conclude that Shias do not predominantly believe in alterations or additions in Qur’an. The mainstream Shias of today say that they believe in whole Qur’an from al- Fatiha to An- Naas. However the blunder of Twelver Shias is that they do not declare their scholars as Kafirs (disbelievers) who believed and still believe that Qur’an is tampered.

al-islam.org is the most renowned Shia website, in it they have written in detail about Shia belief in the infallibility of the Qur’an.

They narrate: Abu Ja‘far Muhammad ibn ‘Ali ibn Husayn Babawayh al- Qummi, known as “Saduq” (d. 381 AH), says:

Our belief regarding the Qur’an is that it is God’s Word and revelation; it is a book which is free from falsehood and incorrectness and it has been sent down by God, the All- wise, and He is its guardian.[Al- I’tiqadat, p.93]

Note: The word Saduq according to Shia is used for their top most scholars.

They also narrate many more hadiths and sayings of their scholars which establish beyond doubt that the Shias do not believe in alterations or additions in Qur’an. You may also refer to Shiapen website where there is a detailed article called “Shia scholars about the completeness of Quran” and they have asserted from overwhelming Shia scholars of past and present that Qur’an is not tampered.

The problem arises when we talk about abrogated verses in the Qur’an. Both Sunni and Shia believe that some verses were revealed to the Prophet but they were not made part of the Qur’an. Moreover, they also believe that the Qur’an was revealed in a different order than the present day Qur’an. Initial verses of Surah al- Alaq were revealed first, but in present Qur’an they are mentioned in 96th chapter. Also the verse of Qur’an which mentions:…”This day I have perfected for you your religion and completed My favor upon you and have approved for you Islam as religion”… (5:3) is considered as last verse of Qur’an although it is present in 5th chapter.

Let us first understand a principle from Qur’an that protector of Qur’an is Allah Himself.

Qur’an states: It is certainly We Who have revealed the Reminder (Qur’an), and it is certainly We Who will preserve it. [Mustafa Khattab: 15:9. Brackets mine]

Qur’an states: Indeed, those who disbelieve in the message after it has come to them. And indeed, it is a mighty Book. Falsehood cannot approach it from before it or from behind it; [it is] a revelation from a [Lord who is] Wise and Praiseworthy. [Sahih International: 41:41, 42]

Qur’an also states: …This day I have perfected for you your religion and completed My favor upon you and have approved for you Islam as religion. But whoever is forced by severe hunger with no inclination to sin - then indeed, Allah is Forgiving and Merciful. [Sahih International: 5:3]

Let us read some hadiths misused to assert that Qur’an is not preserved. It states in Sahih Muslim:

Umar b. Khattab sat on the pulpit of Allah's Messenger (ﷺ) and said: Verily Allah sent Muhammad (ﷺ) with truth and He sent down the Book upon him, and the verse of stoning was included in what was sent down to him. We recited it, retained it in our memory and understood it. Allah's Messenger (ﷺ) awarded the punishment of stoning to death (to the married adulterer and adulteress) and, after him, we also awarded the punishment of stoning, I am afraid that with the lapse of time, the people (may forget it) and may say: We do not find the punishment of stoning in the Book of Allah, and thus go astray by abandoning this duty prescribed by Allah. Stoning is a duty laid down in Allah's Book for married men and women who commit adultery when proof is established, or it there is pregnancy, or a confession. [Sahih Muslim, Hadith # 4194]

This hadith and many other hadiths prove that many verses of the Qur’an were not made part of it, although they were revealed to Prophet (Peace be upon him) at a certain time. This hadith of Sahih Muslim is to be understood from another hadith of Jami’ at- Tirmidhi where Umar (ra) says:

"The Messenger of Allah (ﷺ) stoned, Abu Bakr stoned, and I stoned. If I didn't dislike that I add to the Book of Allah. I would have written it in the Mushaf, for I fear that there will come a people and they will not find it in the Book of Allah, so they will disbelieve in it." [Jami’ at- Tirmidhi: Vol. 3, Book 15, Hadith 1431. Authentic hadith]

Hence Sayyiduna Umar (ra) knew it from the Prophet that verse of stoning was not to be added in Qur’an.

The Shias try to turn the tables by mentioning a hadith which is present in Sahih Bukhari that Abdullah Ibn Mas’ud did not consider the last 2 chapters of the Qur’an to be part of it. According to Ahlus Sunnah, this hadith is a lie no matter it is present in Bukhari or wherever. Remember all the hadiths presented below from Sunni sources are “AHAAD (SINGULAR)” and not Mutawattir (multiply narrated to certainity) and therefore according to Usool (principle) they do not stand a chance in front of Qur’an and logic.

The hadith states:

Narrated Zirr bin Hubaish: I asked Ubai bin Ka`b, "O Abu Al Mundhir! Your brother, Ibn Mas`ud said so- and- so (i.e., the two Mu'awwidh-at do not belong to the Qur'an)." Ubai said, "I asked Allah's Messenger (ﷺ) about them, and he said, 'They have been revealed to me, and I have recited them (as a part of the Qur'an)," So Ubai added, "So we say as Allah's Messenger (ﷺ) has said. [Sahih Bukhari 6.501]

Imam an- Nawawi said:

 أجمع المسلمون على أن المعوذتين والفاتحة وسائر السور المكتوبة في المصحف قرآن. وأن من جحد شيئا منه كفر. وما نقل عن ابن مسعود في الفاتحة والمعوذتين باطل ليس بصحيح عنه

Translation: There is consensus of Muslims that Muawizatain (last two chapters of Qur’an), al-Fatiha and other chapters are written in manuscript of Qur’an, whosoever rejected anything from it is a disbeliever. Regarding what was narrated from Ibn Mas’ud about al- Fatiha and al- Muawizatain (al- falaq and an- naas) then it is false, and not authentic from him”[al- Majmoa sharhul al- Mahzab” (3/396) 

Imam Jalal ud din as- Suyuti (rah) said:

هذا كذب على ابن مسعود وموضوع، وإنما صح عنه قراءة عاصم عن زر عنه، وفيها المعوذتان والفاتحة

It is a lie attributed to Ibn Mas’ud and a fabrication. It is authentically proven from him the Qiraat (recitation) of Asim from Zirr, and in it are Muawizatain and al- Fatiha”. [As- Suyuti in al- Itqaan fi Ulumil Qur’an, where he quotes ibn Hazm’s opinion]

The Qiraat of Aasim, al- Kisai, Hamza, and  Khalaf all prove from Ibn Mas’ud that he recited al- Fatiha and Muawizatain and they were present in his Mushaf.

Plus there are Mudaliseen in one narration that mentions it and in second there is present Asim ibn Abu Nujud who elsewhere narrates Qirat of Ibn Mas’ud which contains al- Fatiha, Surah Falaq, and Surah an- Naas.

Therefore, even if it is mentioned in Bukhari or any other book of hadith still it is to be considered a fabrication and lie.

There is also another troubling hadith in Sahih Muslim which states:

'A'isha (Allah be pleased with, her) reported that it had been revealed in the Holy Qur'an that ten clear sucklings make the marriage unlawful, then it was abrogated (and substituted) by five sucklings and Allah's Apostle (ﷺ) died and it was before that time (found) in the Holy Qur'an (and recited by the Muslims). [Sahih Muslim, Hadith # 3421]

This hadith claims that the verse of 5 suckling was present in Qur’an till the Prophet (Peace be upon him) died. We do not find any such verse in Qur’an today, so how do we answer this hadith? The first answer is that any hadith which contradicts Qur’an is to be outright rejected. The second answer is that Aisha (ra) was not aware of even second abrogation whereas other Sahaba were which is why they never made it part of Qur’an when Qur’an was compiled.

Imam an- Nawawi (rah) said about this hadith:

و بضم الياء من ( يقرأ ) ومعناه أن النسخ بخمس رضعات تأخر إنزاله جدا حتى أنه صلى الله عليه وسلم توفي وبعض الناس يقرأ خمس رضعات ويجعلها قرآنا متلوا لكونه لم يبلغه النسخ لقرب عهده فلما بلغهم النسخ بعد ذلك رجعوا عن ذلك وأجمعوا على أن هذا لا يتلى

There is a dumma on the letter ya'a and it means that the abrogation of the five sucklings came very late until the time that the Prophet (peace be upon him) died and a few people were reciting the five sucklings verse making it part of the Qur'an for they might not have been informed of its abrogation. So when he (Muhammad peace be upon him) did inform them afterwards they stopped reciting it and formed a consensus that this verse should not be recited anymore. [Imam an- Nawawi, Sharh Sahih Muslim, Kitab: Al Ridaa', Bab: Al Tahreem Bi Khams Ridaa'aat]

Allama al- Sindi (rah) said:

قيل إن الخمس أيضا منسوخة تلاوة إلا أن نسخها كان في قرب وفاته صلى الله تعالى عليه وسلم فلم يبلغ بعض الناس فكانوا يقرءونه حين توفي صلى الله تعالى عليه وسلم ثم تركوا تلاوته

It is said that the five's (verse on five sucklings) recitation has been abrogated and its abrogation came near the death of the Prophet (peace be upon him) so some people weren't informed about it. So they used to recite it but when the Prophet (peace be upon him) died they left its recitation. [Al Sindi, Sharh Sunan al Nisaa'i, Kitab: Al Nikah, Bab: Al Qadar Allazhi Yuharrim Min Al Ridaa'aa, Commentary on Hadith no. 3255]

Shams ul Haq Azeemabadi said:

المعنى أن النسخ بخمس رضعات تأخر إنزاله جدا حتى أنه صلى الله عليه وسلم توفي وبعض الناس يقرأ خمس رضعات ويجعلها قرآنا متلوا لكونه لم يبلغه النسخ لقرب عهده فلما بلغهم النسخ بعد ذلك رجعوا عن ذلك وأجمعوا على أن هذا لا يتلى . والنسخ ثلاثة أنواع : أحدها ما نسخ حكمه وتلاوته كعشر رضعات . والثاني ما نسخت تلاوته دون حكمه كخمس رضعات

And what this means is that the abrogation by five sucklings was revealed very late to the extent that when the Prophet (peace be upon him) died, some people were still reciting the verse of five sucklings and making it part of recited Qur'an for they were not informed about its abrogation but when they were after that, they went back on that and formed a consensus on that this verse must not be recited. And abrogation is of three types: One of them is that its ruling and recitation be abrogated just like the ten sucklings verse. And the second is that its recitation has been abrogated without its ruling just like the five sucklings verse... (Muhammad Shams al- Haqq al- Azeem Abadi, Awn al- Mabud Sharh Sunan Abu Dawud, Kitab: Al Nikah, Bab: Hal Yuhharram Ma Doona Khamsa Ridaa'aat, Commentary on hadith no. 1765]

Another hadith which is found in Ibn Majah is even more troublesome. It has been seen that some ignorant Sunnis accuse the Shias of believing that parts of Qur’an were eaten by some goat. To the surprise of such ignorant Sunnis a hadith is actually present in our own Sunni literature authenticated by Salafi Dar us Salam version that a sheep ate some verses of Qur’an

The hadith states: It was narrated that 'Aishah said: “The Verse of stoning and of breastfeeding an adult ten times was revealed, and the paper was with me under my pillow. When the Messenger of Allah died, we were preoccupied with his death, and a tame sheep came in and ate it.” [Sunnan Ibn Majah, Book 9, Hadith 2020. Falsely declared “Hasan (good)” in Salafi Dar us Salam version]

The additional wording of “tame sheep eating the paper of Qur’anic verses” only comes from narrator Muhammad bin Ishaq. He has been criticized by many Muhaditheen. Imam Malik (rah) even called him a “Grand Liar (Dajjal)” therefore the hadith will become Shadh (odd) and weak. Salih Munnajad the Salafi scholar of islamqa also rejected this hadith [See: islamqa.info/en/175355]

Another hadith misused is:

Abu Harb b. Abu al- Aswad reported on the authority of his father that Abu Musa al- Ash'ari sent for the reciters of Basra. They came to him and they were three hundred in number. They recited the Qur'an and he said: You are the best among the inhabitants of Basra, for you are the reciters among them. So continue to recite it. (But bear in mind) that your reciting for a long time may not harden your hearts as were hardened the hearts of those before you. We used to recite a surah which resembled in length and severity to (Surah) Bara'at. I have, however, forgotten it with the exception of this which I remember out of it:" If there were two valleys full of riches, for the son of Adam, he would long for a third valley, and nothing would fill the stomach of the son of Adam but dust." And we used so recite a surah which resembled one of the surahs of Musabbihat, and I have forgotten it, but remember (this much) out of it:" Oh people who believe, why do you say that which you do not practise" (lxi 2.) and" that is recorded in your necks as a witness (against you) and you would be asked about it on the Day of Resurrection" (xvii. 13). [Sahih Muslim # 2286]

This hadith creates serious problems. It claims that there was a Surah resembling length of Surah Bara’at (Chapter 9) and a Surah resembling like Surahs of Musabbihat. Abu Musa (ra) then recites two verses, first of which is totally not present in Qur’an today and second one having last wording is not found in Qur’an either. 

The first answer is again that any hadith which contradicts Qur’an is to be outright rejected. Secondly this narration is “AHAD (SINGULAR)” and not “MUTAWATIR (MULTIPLY NARRATED)” whereas Qur’an is proven from Tawatur (multiple chains of transmission and continuous memorization of it which has been going on from the time of Prophet till today) and singular narrations are never taken as proof on belief issues.

It is also an opinion of Hanafi and Maliki schools that Bismillah is not part of Surah al- Fatiha nor beginning of other Surahs. Salafi scholar Aasim al Hakeem also says so. Salih al Uthaymeen the leading Salafi scholar says Bismillah is not part of al- Fatiha [Majmu‘ Fataawa ash- Shaykh Ibn ‘Uthaymeen (13/109)]

However all four schools believe that it is part of Surah Naml Verse # 30. The Shafis believe it is part of al- Fatiha and also beginning part of all Surahs except Surah at- Tawba. They use this following verse as proof: And We have certainly given you, [O Muhammad], seven of the often repeated [verses] and the great Qur'an. [Sahih International: 15:87]

Read Tafsir Ibn Kathir under Surah Fatiha for details. Also read Tibyan ul Qur’an of Allama Ghulam Rasool Sa’eedi, Volume # 1. These opinions do not hint towards Tahrif in Qur’an because except for al- Fatiha the Bismillah is not written as verse of other Surahs in beginning, nowhere in the Quran is Bismillah written as verse # 1 of other Surahs. The Bismillah is just a separator between Surahs as this authentic hadith states:

Ibn Abbas said: The prophet (ﷺ) did not distinguish between the two surahs until the words “In the name of Allah, the Compassionate, the Merciful” was revealed to him. These are the words of Ibn al- sarh. [Sunnan Abu Dawud, Hadith # 787. Hadith is authentic and also declared authentic by Ibn Kathir in his Tafsir under Bismillah]

Hence Bismillah is just a separator between Surahs and it does not matter if scholars differed whether it is part of beginning of other Surahs or not. Although I am a Hanafi but I disagree with the opinion of Hanafis, Malikis, and Salafi authorities like Ibn Uthaymeen and Aasim al Hakeem that Bismillah is not part of al- Fatiha. Qur’an has come to us through Tawatur and Bismillah is present as first verse of al- Fatiha and is also written before all Surahs except Surah at- Tawba. Having said that the predominant opinion of Sunnis is that it should be recited silently in prayer.

Reconciliation: The mainstream Shia scholarship and knowledgeable among them assert that Qur’an is free from alterations/forgeries or additions. There are narrations in Shia books that mention Tahrif (insertions or deletions) but Shia consider them to be forged/weak. However Tafsir al Qummi the classical and most authentic Shia Tafsir says about following verses:

Lo! Allah preferred Adam and Noah and the Family of Abraham and the Family of 'Imran above (all His) creatures (Pickthall: 3:33)

Ali bin Ibrahim al Qummi, the famous and classical shi’ite commentator of Quran said regarding this verse

وقال العالم عليه السلام نزل " وآل عمران وآل محمد على العالمين " فاسقطوا آل محمد من الكتاب.

The Imam alayh salam said: This ayah was revealed having the words i.e. The Family of Imran and “THE FAMILY OF MUHAMMAD ABOVE ALL PEOPLE” but (this last part) was removed from the Kitab (Qur’an) [Tafsir ul Qummi under 3:33]

Note: There are even some Sunni narrations which assert that Ibn Mas’ud’s Mushaf contained the extra wording: “The family of Muhammad above all people” [Tafsir Bahr al Muheet by Abu Hayyan al Andalusi (2/203). Also Tafsir al Thalabi called Kashf al Bayan 8/249, however the report is extremely weak and could be called fabricated too as Naseebi narrates Manakeer from Shia and fabricates for them. Abu Janada is accused of lying].

After consulting some Shia researchers it has to be accepted that this addition in verse was written as an explanatory note in Qur’an and was not part of verse. The Sahaba used to do this to Mushaf of Qur’an too, hence Shia cannot be accused of Tahrif.

Quran states: That is because they hate the Revelation of Allah; so He has made their deeds fruitless (Yusuf Ali: 47:9)

The same Al- Qummi says:

عن أبي جعفر عليه السلام قال: نزل جبرائيل على محمد صلى الله عليه وآله بهذه الآية هكذا ذلك بأنهم كرهوا ما أنزل الله في علي - إلا أنه كشط الإِسم - فأحبط أعمالهم

From Abi Jafar (i.e. Imam Baqir) who said: Jibril (a.s) brought this verse to Muhammad (salallaho alaihi wasalam) as: That is because they hate the “REVELATION ABOUT ALI” but the apostates removed Ali's name (from the Quran).[Tafsir al Qummi under 47:9]

Shia researchers say that even this example does not prove Tahrif. They say that Qur’an was revealed with Ta’weel also and Shaykh Qummi is talking about revelation of Ta’weel in this verse.

Here is one example from high ranking shia book of hadith which even their scholars accepted to be authentic.

علي بن الحكم ، عن هشام بن سالم ، عن أبي عبد الله ( عليه السلام ) قال إن القرآن الذي جاء به جبرئيل ( عليه السلام ) إلى محمد  صلى الله عليه وآله  سبعة عشر ألف آية .

Narrated by Ali bin al- Hakm, he narrated from Hishaam bin Saalim, he narrated from Abi Abdullah (alayh salam) that he said: The Qur’an which Gabriel (a.s) brought to Prophet Muhammad (Peace be upon him) had 17,000 verses. [Ash- Shafi translation of al- Kafi by Shia Muhadith Muhammad bin Ya’qub al- Kulayni, Kitab Fadhl al- Qur’an, Chapter # 14 (Baab ul Nawadir) Published by Zafar Shameem Publications Nazim Abad Karachi, Pakistan]

The leading Shia hadith experts said about this narration:

Mullah Baqir al- Majlisi said: This hadith is “Muwathaq (relied upon)” [Mir’at al- Uqool (12/525)

Al- Amili another Shia hadith expert said: This hadith is Authentic. [Al- Fuw’aid al- Toosiyah, Page # 483]

After consulting some Shia researchers it was known that they do not consider this narration as authentic and call the above two scholars as mistaken. They also say that some manuscripts of al- Kafi say 7,000 in stead on 17,000. According to mainstream Ahlus Sunnah the total number of verses in Qur’an is 6,236. Shia researchers say that extra 764 verses were exegesis or interpretations which were revealed too but were not made part of Qur’an.

Similarly the narrations in Sunni books as some of them were mentioned above are used against Sunnis by Shias rather by non- Muslims against Islam. We have explained those narrations clearly and we Sunnis believe whosoever says Qur’an is tampered is a Kafir (disbeliever).

We have to come to conclusion that no book whether Bukhari, Muslim, al- Kafi, or Tafsir al- Qummi stand a chance in front of Qur’an. The hadiths in this regard have to be thrown away both by Sunnis and Shias. Also Ahlus Sunnah firmly believe that Qur’an is not altered nor tampered, Shia should also be given benefit of the doubt and narrations in their books should be considered false as Shia claim today. However those twelver Shia scholars who believed in Tahrif of Qur’an were Kafirs and should be declared as such by Twelver Shia too.