The Bible versus the Qur'an
While Muhammad is evidenced as believing that the Bible was inspired and given by God, and the relatively brief Qur'an depends upon the Bible in its allusions to it, abundant critical differences exist between the two books, perhaps due to Muhammad's alleged illiteracy and dependence upon similarly biblically illiterate and confused sources.
The Islamic solution to this has typically been to assert the Bible was altered after Muhammad's time. However the wealth of manuscripts, including those who antedate the giving of the Qur'an, disallow that attempt.
Distinctions between the Bible and the Qur'an
At less than 80,000 words, (figures vary: 77,701 in Arabic by one source, 77,439 by ‘Ata bin Yasar) the Qur'an is much smaller than the Bible, (602,585 words in the Old Testament; 180,552 in the New = 783,037, with the total words in just the verses in the KJV being counted at 788,258.) The Qur'an is also far more restrictive in in its scope of communication, lacking the manner of extensive historical narratives of the Bible, and the context it provides for its commands, as well as genealogical records which helps provide historical chronology. In addition, absent from the Quran are extended doctrinal discourses on salvation, such as are especially seen in the New Testament. This results in difficultly formulating broad systematic theology out of the Qur'an by itself, and its allusions to Biblical characters and events evidences that it requires knowledge of the Bible, which as the prior revelation, it must agree with.
Muhammad's referencing and contradictions of the Bible
Early Islam and Muhammad himself is seen to uphold the Scriptures that existed then as divinely inspired, both the Torah, (Sura 2:87) and the Psalms, (4:163) and the Gospels, (Suras 3:3; 5:46) such as in stating,
How come they unto thee for judgment when they have the Torah, wherein Allah hath delivered judgment (for them)? Yet even after that they turn away. Such (folk) are not believers. (Sura 5:43; Pickthall)
And We sent after them in their footsteps Isa [Jesus], son of Marium, verifying what was before him of the Taurat [Torah] and We gave him the Injeel [Gospel] in which was guidance and light, and verifying what was before it of Taurat and a guidance and an admonition for those who guard (against evil). (Sura 5:46; Shakir)
Say: "O People of the Book! ye have no ground to stand upon unless ye stand fast by the Law, the Gospel, and all the revelation that has come to you from your Lord, (Sura 5:68; Y. Ali)
If thou wert in doubt as to what We have revealed unto thee, then ask those who have been reading the Book from before thee: the Truth hath indeed come to thee from thy Lord: so be in no wise of those in doubt. (Sura 10:94 (Y. Ali)
And dispute ye not with the People of the Book, except with means better (than mere disputation), unless it be with those of them who inflict wrong (and injury): but say, "We believe in the revelation which has come down to us and in that which came down to you; Our Allah and your Allah is one; and it is to Him we bow (in Islam). (Sura 29:46; Y. Ali)
Sura 6:34 also states that "there is none that can alter the words (and decrees) of Allah." (Y. Ali)
However, the Qur'an critically contradicts the Bible, especially as concerns the person and work of Jesus Christ, as it flatly denies His death and resurrection, as well as His divine nature, both of which which are held by Christians to be abundantly testified to.
Charges of textual corruption
Islamic apologists recognize these contradictions, and respond by invoking Surah 2:78-79 which speaks of "illiterates, who know not the Book....who write the Book with their own hands" as evidence that the Bible was tampered with.
Christian apologists respond to these charges by pointing out that the Qur'an itself affirms the integrity of The Book, thus if corruption occurred then it would be in contradiction to the Qur'an itself, and its doctrine of the preservation of Divine revelation. And that the amount of alterations required to explain the Quranic deviations from Biblical text would require a significant amount of changes to the Old Testament and virtually a complete rewriting of the New, yet for such a project there is no manuscript evidence, but the contrary exists for its preservation from such changes.
An abundance of manuscripts which predate the Quran yet exist, including the Codex Sinaiticus (c. 350 AD), with Aland numbering a total of 230 extant New Testament manuscript portions which pre-date 600 AD (192 Greek New Testament manuscripts, 5 Greek lectionaries containing scripture, and 33 translations of the Greek New Testament).
Archaeological evidence also evidences that manuscripts from the first century could last well over a hundreds of years, and that retired and discarded manuscripts were not altered.  The doctrinal conflation of early manuscripts with later ones manifests that no such manner of alterations or rewriting such as Islam assets took place,  and even the variations among manuscripts (mainly in spelling or sentence structure and other thing which do not change doctrine) help to confirm the reliability of the Biblical texts more than the Islamic choice to burn versions which have variant readings.
In addition, what further disallows the Islamic theory is that none of the thousands of all extant Biblical manuscripts even from before the time of Muhammad agree with the Qur'anic contradictions of Scripture.
It is also postulated that if Muhammad could not read, as Islam states, then he would have relied upon the word of others (travelers, etc.) who were overall likely to be significantly Biblically illiterate. This would explain how Muhammed could believe such things as the Christian Trinity consisting of God, Jesus and Mary, (Sura 5:116-117) in addition to speaking numerous contradictions of the Bible.
In response, Muslim apologists also seek to make a case against a reliable Bible based upon the lack of a universal canon among all Christian churches, or early incomplete manuscripts, or additions to them (the Epistle of Barnabas, and portions of The Shepherd of Hermas to Codex Sinaiticus), as well a relatively small degree of actual (beyond spelling, etc.) textual disagreement among some of the thousands of existing manuscripts. However, none of these aspects provides a solution to the Islamic problem, as none of the manuscripts substantiate the Qur'anic deviations, nor does the small percentage (contrary to typical Muslim exaggeration) of actual variants among manuscripts support the manner of massive changes which the Islamic solution requires. Moreover, the Qur'an, for which there is no manuscripts evidence for over 100 years after it was said to be given, evidences its own problematic texts, even though it is a far smaller (in size and scope) book, and one that was written after durable writing materials came into use, and then underwent a purification process in which variant manuscripts were burned. One researcher concludes,
- Manuscript, as well as documentary and archaeological evidence indicates that much of what the Qur'an maintains does not coincide with the historical data at our disposal which comes from that period. 
Thus it is seen that the manner of corruption of biblical text which Islam charges is that of the Qur'an, not the Bible which authority it is much based upon, and Muhammad must be charged as being one who attempted to corrupt The Book.
While Muslims also typically claim that the text of the Qur'an is identical to that received by Muhammad, Christian researchers contend that there is overwhelming evidence that it is not. 
Although the Qur’an manuscripts exhibit a notable stability in the text across many centuries, evidence supports the conclusion that considerably greater diversity existed among the earlier texts of the Qur’an than is reflected in the extant manuscripts studied thereafter. As is widely accepted, in the late 7th century, the Caliph Uthman, being disturbed by the diversity in the text of the Qur’an, organized a standardization of the Qur’anic manuscripts, destroying texts considered deviant, and thus cutting off access to possibly more original forms of the text of the Qur'an. Further steps were taken in successive centuries to fix the text and its recitation. The result of textual examination of Qur’anic manuscripts leads Keith E. Small, Phd. author of Textual Criticism and Qur’an Manuscripts, to conclude,
|“|| Though Muslims may take pride in the fidelity of the preservation of this text, it does not reproduce precisely what was originally considered to be the Qur'an' in the early seventh century. Because of the standardizations of the text in 653-705/33-86 AH and 936/324 AH, together with the constant pressure throughout Islamic history to have one text match their dogma, many texts which had equally good claims to containing authentic readings were suppressed and destroyed.
And, because of the emphasis on oral transmission and the vagaries of Arabic as it developed, the written text was constantly vocalized in new ways which did not preserve the original vocalization. The original vocalization must have been lost very early on if it did indeed exist.
While bearing testimony to the careful preservation of one particular consonantal text, the history of the transmission of the text of the Qur'an is at least as much a testament to the destruction of Qur'an material as it is to its preservation. It is also testimony to the fact that there never was one original text of the Qur'an'.
Gospel of Barnabas
As no extant Biblical manuscript, from before the time of Muhammed or after him, agrees with the Quranic contradictions, many Muslim apologists look to the Gospel of Barnabas for support. However, this radically different account is judged by both Christian and secular academics (and even some Muslims such as Abbas el-Akkad) to be a late work and pseudepigraphical. With its obvious anachronisms and historical errors (like sailing to Nazareth) and utter lack of early manuscript evidence and irreconcilable differences between it and any ancient manuscripts, it is manifest to be a fourteenth century attempt to read Islamic doctrine into the Bible, which clearly refutes it.  
Principal areas of disagreement
The primary issues in which the Qur'an radically fails to conflate with the Bible are in regard to the person and work of Christ, as well as the nature of the people of God, and the means by which their mission is carried out.
While the Bible systematically reveals the Messiah as being the Divine Son of God, the Qur'an flatly denies this, but relegates Christ to being a most perfect messenger of God. While the Bible predicts and clearly records and abundantly references the death and resurrection of Christ,  that He sacrificially shed His blood and died on the cross, in order to make the perfect atonement for man's forgiveness, and rose to life and later ascended to the right hand of the Father, the Qur'an dismisses this, and offers a brief explanation that a substitute took His place.(Sura 4:157) As the entire message of the New Testament centers around Jesus Christ being the unique son of God - a title which itself conveyed Deity at that time (Jn. 5:18; 19:7) - who died and rose again and now reigns as the present savior and future judge of mankind, then the Bible and the Qur'an are most irreconcilable on these points.
In addition, in the New Testament the nature of the people of God is essentially that of a spiritual entity, into which "body" all believers are baptized upon believing, (1 Cor. 12:13) and are translated into the spiritual kingdom of Christ. As such, the means of warfare for the New Testament church was "not carnal", that is, by the sword of men, but spiritual: "By pureness, by knowledge, by longsuffering, by kindness, by the Holy Ghost, by love unfeigned, By the word of truth, by the power of God, by the armour of righteousness on the right hand and on the left." (2 Cor 6:6-7) In contrast, Islam works out of the model of a seventh century physical theocracy, which thus uses physical means of oppression toward those without as well as within, in order to defeat its enemies and enlarge its borders. Due to both the nature of the Qur'an, and Muhammad's example, and evidence from the Hadityh, many believe that “radical” Islam is more historically authentic and representative of the modern Islamic world than the “moderate” variety.
Muslims respond to such by repeating atheism's allegations of irreconcilable contradictions within the Bible, which Christians respond to by providing clarifications and explanations, while also documenting various other contradictions between the Bible and the Qur'an, as well as within the later, and between the latter and other authorities.
While there exists within liberal Christianity those who seek to harmonize the two religions, as well as a form of liberal Islam which seeks to minimize differences, such results in a denial of truth, as well as freedom of religion in the long term. Patrick Sookhdeo, the director of the Institute for the Study of Islam and Christianity, warned that the Western Church’s growing tendency to blur theological differences and not uphold the absolute truth is contributing to the threat of radical Islam to the Western World. Sookhdeo, a former Muslim and adviser to British, American and NATO military officials on jihadist ideology, and director of the Barnabas Fund which works with the persecuted church, stated,
- When faced with the uniqueness of Christ we become inclusive. He loves everybody so we talk about love, and hell and damnation goes out the window, said Sookhdeo. It becomes too embarrassing. So our church has conformed itself according to society.
- If the U.S. church goes the way of Europe and embraces liberalism in its theology then it will embrace liberalism in its life,... And if it embraces liberalism in its life then the church will die, and not only will the church die, but society around it will also die.
The past institutionalization of the church and Islamization of most of Asia Minor, where the seven churches of Revelation were located, are seen by some as examples of dangers now being faced.
- based upon critical doctrinal conformity, these numbers would be much smaller, such as in Christianity: http://www.barna.org/barna-update/article/12-faithspirituality/15-christianity-is-no-longer-americans-default-faith
- The Qu'ran: The Scripture of Islam; A. THE COMPOSITION AND CHARACTER OF THE QUR'AN
- answering-islam.org; Contradictions in the Qur'an; Verses contradicting the earlier revelations
- MUHAMMAD VERSUS JESUS CHRIST; Death and Resurrection proclaimed
- The DEITY of CHRIST
- Refuting the Muslims Polemics
- Kurt and Barbara Aland, 1987:82-83
- How Long Were Biblical Manuscripts in Use?
- "Is there much Evidence for the Bible's Reliability?"
- Jochen Katz, My Questions to Muslims; Answering Islam
- TEXTUAL HISTORY OF THE KORAN
- Textual answering-islam.org; Variants of the Qur'an
- Keith E. Small, Textual Criticism and Qur’an Manuscripts, (Lanham/Boulder/New York/Toronto/Plymouth: Lexington Books, 2012), p. 180
- MUHAMMAD VERSUS JESUS CHRIST
- Isa. 53:10-12; Dan. 9:24; Dan. 9:26; Mat. 12:40; 16:21; 20:28; 27:2-10,40,63; Mar. 15:1,16-20; 17:23; Luk. 22:26-27; 23:1-5; 24:7,26-27; Jn. 2:19; 3:14; 8:28-38; Act. 3:13-16; 1Co. 15:3-7; 2Co. 5:21; Gal. 3:13; Phi. 2:5-8; 1Ti. 3:4-6; 2:14; Heb. 5:8; 1Pt. 1:19; 2:24; 3:18,22
- Contradictions in the Qur'an
- christiantoday.com Saturday, February 9, 2008