Though this was also a reply in another thread, it is a discussion of its own as well.
The following quotations summarize Shi’ah beliefs regarding alterations in the words and verses of the Quran.
Shi’ah commentaries of the Quran and their books of “hadith” cite innumerable examples of alleged alterations within the Quran. All of these “alterations” deal exclusively with the attributes of Ali and his descendants, whom the Shi’ahs consider their imams. If one were to collect all of these citations, he would end up with an entirely new Quran. The following are sufficient to give a glimpse of Shi’ah claims in this regard.
Surah al-Baqarah
“And if you are in doubt about what We have sent down upon Our Servant *, then produce a surah the like thereof and call upon your witnesses * other than Allah, if you should be truthful.” Surah al-Baqarah, (2:23)
Alteration:
The commentary given about this verse is that Imam Ja’far as-Sadiq said: “Gabriel brought this verse [to Prophet Muhammad] mentioning Ali as follows: ‘If you are in doubt as to what We have sent down to Our servant regarding Ali…’” Usul al-Kafi.
Surah al-Baqarah again
“But those who wronged changed [those words] to a statement other than that which had been said to them, so We sent down upon those who wronged a punishment * from the sky because they were defiantly disobeying.” Surah al-Baqarah(2:59)
Alteration:
Imam al-Baqir said: “Gabriel brought this verse to the Prophet (SAW) as follows: ‘But those who usurped the rights of the Prophet’s family members changed the words that were said to them, so We down on those who usurped the rights of the Prophet’s family members a punishment from the sky because they were defiantly diobeying.’” Usul al-Kafi
Surah an-Nisa
“O you who have been given the Scripture, believe in what We have sent down [to Muhammad (SAW)], confirming that which is with you, before We obliterate faces and turn them toward their backs or curse them as We cursed the Sabbath-breakers. And the decree of Allah is [always] accomplished.” Surah an-Nisa, (4:47)
Alteration:
Shi’ah traditions state that Gabriel brought this verse to the Prophet (SAW) as follows: “O people, believe in what We have sent down about Ali, confirming what is with you…'” Usul al-Kafi, p.515
Surah an-Nisa
“But if they had done what they were instructed, it would have been better for them and a firmer position [for them in faith].” Surah al-Nisa (4:66)
Alteration:
Imam al-Baqir said: “This verse was revealed as follows: ‘But if they had done what they were [actually] told about Ali, it would have been better for them…’” Usul al-Kafi, vol. 1, p.251
Surah an-Nisa
“But Allah bears witness to that which He has sent down to you. He has sent it down with His knowledge, and the angels bear witness [as well]. And sufficient is Allah a Witness.” Surah an-Nisa, (4:166)
Alteration:
In Tafseer al-Qummi is a narration attributed to Ja’far as-Sadiq that this verse was revealed to the Prophet (SAW) as follows: “But Allah bears witness to that which He has sent down to you concerning Ali, He has sent it down with His knowledge…'” Translation and Commentary of Quran, p.124
Surah an-Nisa
Indeed those who disbelieve and commit injustice - never will Allah forgive them, nor will He guide them to a path." Surah an-Nisa (4:168)
Alteration:
Al-Kulayni related from Imam al-Baqir: “Gabriel revealed this verse to the Prophet (SAW) as follows: ‘Those who usurp the rights of the Prophet’s family - never will Allah forgive them…’” Usul al-Kafi.
It is also narrated in Tafseer al-Qummi that Abu Abdullah (Imam Ja’far as-Sadiq) recited this verse as follows: “Those who disbelieved and usurped th right of Prophet’s family member - never will Allah forgive them…” Translation and Commentary of Quran, pp. 124-125
Surah an-Nisa
“O mankind, the Messenger has come to you with the truth from your Lord, so believe; it is better for you. But if you disbelieve, then indeed, to Allah belongs whatever is in the heavens and earth. And Allah is ever Knowing and Wise.” Surah an-Nisa, (4:170)
Alteration:
The translation of the Quran by the learned Shi’a scholar Maqbul Ahmad (Translation and Commentary of Quran) and the famous scholar al-Majlisi has rendered this verse as follows: “O mankind, the Messenger has come to you with the truth from Allah regarding the wilayah (succession) of Ali…'” Hayat al-Qulub, vol. 3, p, 355
Surah al-Hijr
“[Allah] said, ‘This is a way to Me [that is] straight.’” Surah al-Hijr, (15:41)
Alteration:
Imam Ja’far as-Sadiq said: “This verse was recited as follows: ‘This way of Ali is straight [to Me].’” Usul al-Kafi, vol. 1, p. 521
Surah al-Nahl
“And be not like a woman who untwisted her spun thread after it was strong [by] taking your oaths as [means of] deceit between you so that an Ummah * may be more plentiful than another Ummah.” Surah an-Nahl, (16:92)
Alteration:
According to the Shi’ah tradition, this verse ws revealed to the Prophet (SAW) as follows: “And be not like a woman who untwisted her spun thread after it was strong [by] taking your oaths a [means of] deceit between you lest one Ummah should be more virtuous than your Imams.” The narrator said, “The word Surah an-Nahl is Ummah [and not a immah], but he [the Imam] aswered, 'No, it is a ‘Immah.’” Usul al-Kafi, vol. 1, p.377. “*An Immah” is the plural of “Imam.”
Surah al-Kahf
“And say, ‘The truth is from your Lord, so whoever wills - let him believe; and whoever will - let him disbelieve.’ Indeed, We have prepared for the wrongdoers a fire whose walls surround them.” Surah al-Kahf, (18:29)
Alteration:
Abu Ja’far said that Gabriel brought this verse to the Prophet (SAW) as follows: “The truth is from your Lord concerning the wilayah (succession) of Ali, so whoever wills - let him believe; and whoever wills - let him reject the Prophet’s family members. Indeed, We have prepared for the wrongdoers a fire…” Usul al-Kafi, vol. 1, p. 53; Hayat al-Qulub, vol. 3, p.215
Surah Ta Ha
“And We had already taken a covenant from Adam before, but he forgot; and We did not find in him determination.” Surah Ta Ha, (20:115)
Alteration:
Imam Ja’far as Sadiq said: “The ‘covenant’ was concerning Muhammad (SAW), Ali, Fatimah, al-Hasan and the Imams from among their descendants. Adam forgot them. By Allah, this verse was revealed to Muhammad (SAW) as follows: ‘We had already taken a covenant from Adam before concerning Muhammad, Ali, Fatimah, al-Hasan, al-Husayn, and the Imams from among [their] descendants, but he forgot.’” Usul al-Kafi, vol 1. p.153
Surah al-Ahzab
“He * will Amend for you your deeds and forgive you your sins. And whoever obeys Allah and His Messenger has certainly attained a great attainment.” Surah al-Ahzab, (33:71)
Alteration:
In Usul al-Kafi and Tafseer al-Qummi it is narrated fro Imam Ja’far as-Sadiq that this verse was revealed as follows: “He will amend for you your deeds and forgive your sins. And whoever obeys Allah and His Messenger regarding the wilayah (succession) of Ali, and his imams has certainly attained a great attainment.” Translation and Commentary of Quran, p.512
Surah ash-Shura
"Difficult for the polytheists is that to which you invite them. Allah chooses for Himself whom He wills and guides to Himself whoever turns back [to Him]. Surah ash-Shura, (42:13)
Alteration:
Imam ar-Ridha said that Allah’s actual words in the Quran were: “Difficult for those who deny the wilayah of Ali is that to which you invite them.” Usul al-Kafi, vol. 1, p.514
Surah al-Ahqaf
“Say, I am not something original among the Messengers, nor do I know that will be done with me or with you. I only follow that which is revealed to me, and I am not but a clear warner.'” Surah al-Ahqaf, (46:9)
Alteration:
According to Shi’ah “hadiths” this verse was revealed as follows: “I am not something original among the Messengers, nor do I know what will be done with me or with you. I only follow that which is revealed to me regarding Ali, and I am not but a clear warner.” Translations and Commentary of Quran, p.602
Surah Muhammad
“That is because they said to those who disliked what Allah sent down, ‘We will obey you in part of the matter.’ And Allah knows they conceal.” Surah Muhammad, (47:2)
Alteration:
According to Shi’ah tradition, Gabriel brought this verse to the Prophet (SAW) as follows: “That is because they said to those who disliked what Allah sent down to the Prophet concerning Ali, ‘We will obey you in part of the matter.’ And Allah knows what they conceal.” Usul al-Kafi, vol.1, p.516
Surah adh-Dhariyat
“Indeed, you [disbelievers] are in discordant speech. Deluded away from it * is he who is deluded.” Surah ad-Dhariyat, (51:8-9)
Alteration:
Imam Muhammad al-Baqir said that this verse was revealed to the Prophet (SAW) as follows: “Indeed, you are in discordant speech concerning the wilayah (successsion) of Ali.” He added, “He who denies the wilayah of Ali is deprived of Paradise.” Usul al-Kafi, vol 1., p. 518
Surah al-Mulk
“Say, ‘He is the Most Merciful; we have believed in Him, and upon Him we have relied. And you will know who it is that is in manifest error.’” Surah al-Mulk, (67:29)
Alteration:
Imam Ja’far as-Sadiq said in explanation of this verse: “The Prophet (SAW) said, ‘And you will know who it is that is in manifest error, O disbelievers! I had informed you of the wilayah of Ali after me. Now who is in clear error’ This explanation was revealed with the verse.” Usul al-Kafi, vol. 1, p.517
Surah al-Ma’arij
“A questioner asked about a punishment bound to happen to disbelievers; of it there is no preventer. [It is] from Allah, owner of the ways of ascent.” Surah al-Ma’arij, (70:1-3)
Alteration:
Imam Ja’far as-Sadiq said that this verse was revealed to the Prophet (SAW) as follows: “A questioner asked about a punishment bound to happen to the disblievers for denying the wilayah of Ali, of which there is no preventer.” Usul al-Kafi, vol. 1, p.518*
*Surah al-Muzzammil
“And leave Me [to deal] with the deniers, those of ease [in life], ad allow them respite a little.” Surah al-Muzzammil,(73:11)
Alteration:
Usul al-Kafi contains a narration by Imam Musa al-Kathim that this verse was revealed to the Prophet (SAW) as follows: “And leave Me [to deal] with the deniers of your will concerning the wilayah (succession of Ali), those of ease, and allow them respite a little.” Translation and Commentary of Quran, p. 688
Surah al-Wilayah
A number of Shi’ah scholars claim that the Quran once contained a chapter entitled, “al-wilayah” (“Succession”), wherein Al-Mighty Allah mentioned Ali’s name and declared his immediate succession and imamate after Prophet Muhammad (SAW). Muhsin al-Kashmeeri, a Persian scholar, has published this alleged Surah of seven verses in his book Dabastan-e-Mazahib. Several editions have been printed and are available in Iran. Allamah Nuri at-Tabrisi has also mentioned in his book {Fasl al-Khitab, p.22} that the chapter al-wilayah declaring Ali’s imamate has been deleted from the existing Quran. Professor Noeldek in his History of Quran, vol. 2, p. 102 has reproduced this chapter (Surah) from the Persian book Dabastan-e-Mazahib. The same is reproduced below.
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O you who believed, believe in the Prophet and in the wali (successor), both of whom We sent to lead you to a straight path.
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The Prophet and the wali - they are of one another, and I am the Knowing, the Aware.
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Indeed, those who fulfill the covenant of Allah will have Gardens of Pleasure.
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And those who, when Our verses are recited to them are, of Our verses, deniers -
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For them in Hell is a terrible position when they will be called, “Where are the unjust, the deniers of the messengers?”
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He did not create the Messengers except in truth, and Allah would not manifes them for [only] a short term.
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And exalt with praise your Lord, and Ali is among the witnesses.
Perhaps some readers may consider all these citations old and obsolete. Therefore the writer would like to conclude this discussion with a quote from the recent Shi’ah Imam, Mr. Khoemini, who openly declared ad reemphasized the Shi’ah claim that the Quran had been altered by the Prophet’s companions.
“Those [companions of the Prophet] who cared only for material gains and wordly powers, those who had no interest in Islam or the Quran, and those who exploited the Quran for their own crooked plans - for them it was very easy to delete those verses of the Quran *, to modify the heavenly scripture, and to hide the true Quran from the public eye in such a way that it has become a blot for the entire muslim Ummah until the day of Judgement. The Muslims’ accusation that Christians and Jews altered their heavenly scriptures is proved against the Prophet’s companions as well.” Kashf al-Asrar, p. 111
One can justly ask the followers of Imam al-Khoemini, since they claim that the real Quran does not exist in this world, “What, then is the source of knowledge and guidance for the Shi’ahs?”
The above citations are a few examples of Shi’ah teachings in regard to the Quran. Anyone who is interested in pursuing this matter further may obtain more details from Fasl al-Khitab fi Ithbat Tahreef Kitab Rabb al-Arbab (Conclusive Proof of Alteration in the Book of the Lord of Lords). This is remarkable work of Mirza Husayn bin Taqiyy, a Shi’ah scholar. The author has collected hundreds of “hadiths” from Shi’ah Imams and quotations from Shi’ah scholars for the purpose of showing that the existing Quran has undergone innumerable alterations. When the book was first published in Tehran in 1298 A.H., it caused great uproar and agitation in Shi’ah circles. Shi’ah scholars were much perturbed to see so many of their “hadiths” and quotations openly documented in a book. They realized that their secret doctrines about the Quran were now exposed to the rest of the Muslim Ummah. A number of Shi’ah scholars then hastened to write explanatory notes of the book. A few others openly protested against its publication. The author, Mirza Husayn, later responded to all the objections of Shi’ah scholars in another book, entitled Raddu Ba’dhish-Shubuhati an fasl al-Khitab fi Ithbat Tahreef Kitab Rabb al-Arbab (A refutation of Doubts about Conclusive Proof of Alteration in the Book of the Lord of Lords.) Both these books were so widely acclaimed that when the author died in 1320 A.H., he was given the highest Shi’ah honor and distinction bestowed on anyone: to be buried at Ali’s mausoleum at Najaf in Iraq.
The Shi’ah commentaries on the Quran and books of “hadith” narrations have clearly and repeatedly declared the unauthenticity of the existing Quran, but Shi’ahs still claim to believe in the Quran. It is paradoxical that they derive their faith and beliefs from those same books that deny the authenticity of Quran. One can only explain the disparity between Shi’ah saying and Shi’ah writings on the basis of their practice of Taqiyyah (dissimulation), which encourages Shi’ahs to conceal truth under certain conditions and to declare something they do not believe at all. Thus, it is logical to conclude that what is recorded in Shi’ah books is the true Shi’ah belief, while what Shi’ahs state verbaly is only taqiyyah.
This perhaps explains the reason why Shi’ahs do not memorize the whole of the Quran. On the contrary, the Sunni Muslim Ummah has always produced innumerable huffath (plural of hafiz) who memorize the entire Quran from beginning to end with precise tajweed. Every year in the month of Ramadan, these huffath (memorizers) recite the whole Quran aloud during Taraweeh prayers before congregations of worshippers. The Quran consists of little over 6,000 verses and a total of 244,744 words made up of innumerable lettersand diacritical marks. To memorize all these verses with the necessary detail of phonetics and punctuation would not be humanly possible but for the will of Almighty Allah. Through His special blessing Allah gives this honor to those who have the proper faith and respect for the Quran, while He deprives those who would cast doubts on its authenticity of that blessing.*******