The Quran contains at least 109 verses that call Muslims to war with nonbelievers.  Some are quite graphic, with commands to chop off heads and fingers and kill infidels wherever they may be hiding.  Muslims who do not join the fight are called 'hypocrites' and warned that Allah will send them to Hell if they do not join the slaughter.

These verses are mostly open-ended, meaning that the historical context is not embedded within the surrounding text (as are nearly all of the Old Testament verses of violence).  They are part of the eternal, unchanging word of Allah, and just as relevant or subjective as anything else in the Qur'an.  

Unfortunately, there are very few verses of tolerance and peace to abrogate or even balance out the many that call for nonbelievers to be fought and subdued until they either accept humiliation, convert to Islam, or are killed.  This proclivity toward violence - and Muhammad's own martial legacy - has left a trail of blood and tears across world history.

Qur'an (2:191-193) - "And slay them wherever ye find them, and drive them out of the places whence they drove you out, for persecution [of Muslims] is worse than slaughter [of non-believers]...and fight them until persecution is no more, and religion is for Allah."  There is a good case to be made that the textual context of this particular passage is defensive war, even if the historical context was not.  However, there are also two worrisome pieces to these verse.  The first is that the killing of others is authorized in the event of "persecution" (a qualification that is ambiguous at best).  The second is that fighting may persist until "religion is for Allah."  The example set by Muhammad is not reassuring.

Qur'an (2:244) - "Then fight in the cause of Allah, and know that Allah Heareth and knoweth all things."

Qur'an (2:216) - "Fighting is prescribed for you, and ye dislike it. But it is possible that ye dislike a thing which is good for you, and that ye love a thing which is bad for you. But Allah knoweth, and ye know not."  Not only does this verse establish that violence can be virtuous, but it also contradicts the myth that fighting is intended only in self-defense, since the audience was obviously not under attack at the time.  From the Hadith, we know that Muhammad was actually trying to motivate his people into raiding caravans with this verse.

Qur'an (3:56) - "As to those who reject faith, I will punish them with terrible agony in this world and in the Hereafter, nor will they have anyone to help."

Qur'an (3:151) - "Soon shall We cast terror into the hearts of the Unbelievers, for that they joined companions with Allah, for which He had sent no authority".  This speaks directly of polytheists, yet it also includes Christians, since they believe in the Trinity (ie. what Muhammad incorrectly believed to be 'joining companions to Allah').

Qur'an (4:74) - "Let those fight in the way of Allah who sell the life of this world for the other. Whoso fighteth in the way of Allah, be he slain or be he victorious, on him We shall bestow a vast reward."  The martyrs of Islam are unlike the early Christians, led meekly to the slaughter.  These Muslims are killed in battle, as they attempt to inflict death and destruction for the cause of Allah.  Here is the theological basis for today's suicide bombers.

Qur'an (4:76) - "Those who believe fight in the cause of Allah…"

Qur'an (4:89) - "They but wish that ye should reject Faith, as they do, and thus be on the same footing (as they): But take not friends from their ranks until they flee in the way of Allah (From what is forbidden). But if they turn renegades, seize them and slay them wherever ye find them; and (in any case) take no friends or helpers from their ranks."

Qur'an (4:95) - "Not equal are those believers who sit (at home) and receive no hurt, and those who strive and fight in the cause of Allah with their goods and their persons. Allah hath granted a grade higher to those who strive and fight with their goods and persons than to those who sit (at home). Unto all (in Faith) Hath Allah promised good: But those who strive and fight Hath He distinguished above those who sit (at home) by a special reward,-"  This passage not only criticizes "peaceful" Muslims who do not join in the violence, but it also demolishes the modern myth that "Jihad" doesn't mean holy war in the Qur'an, but rather a spiritual struggle.  Not only is the Arabic word used in this passage, but it is clearly not referring to anything spiritual, since the physically disabled are given exemption.  (The Hadith reveals the context of the passage to be in response to a blind man's protest that he is unable to engage in Jihad).

Qur'an (4:104) - "And be not weak hearted in pursuit of the enemy; if you suffer pain, then surely they (too) suffer pain as you suffer pain..."  Pursuing an injured and retreating enemy is not an act of self-defense.

Qur'an (5:33) - "The punishment of those who wage war against Allah and His messenger and strive to make mischief in the land is only this, that they should be murdered or crucified or their hands and their feet should be cut off on opposite sides or they should be imprisoned; this shall be as a disgrace for them in this world, and in the hereafter they shall have a grievous chastisement"

Qur'an (8:12) - "I will cast terror into the hearts of those who disbelieve. Therefore strike off their heads and strike off every fingertip of them"  No reasonable person would interpret this to mean a spiritual struggle.

Qur'an (8:15) - "O ye who believe! When ye meet those who disbelieve in battle, turn not your backs to them. (16)Whoso on that day turneth his back to them, unless maneuvering for battle or intent to join a company, he truly hath incurred wrath from Allah, and his habitation will be hell, a hapless journey's end."

Qur'an (8:39) - "And fight with them until there is no more persecution and religion should be only for Allah"  From the historical context we know that the "persecution" spoken of here was simply the refusal by the Meccans to allow Muhammad to enter their city and perform the Haj.  Other Muslims were able to travel there, just not as an armed group, since Muhammad declared war on Mecca prior to his eviction.  The Meccans were also acting in defense of their religion, since it was Muhammad's intention to destroy their idols and establish Islam by force (which he later did).  Hence the critical part of this verse is to fight until "religion is only for Allah."

Qur'an (8:57) - "If thou comest on them in the war, deal with them so as to strike fear in those who are behind them, that haply they may remember."

Qur'an (8:59-60) - "And let not those who disbelieve suppose that they can outstrip (Allah's Purpose). Lo! they cannot escape.  Make ready for them all thou canst of (armed) force and of horses tethered, that thereby ye may dismay the enemy of Allah and your enemy."

Qur'an (9:5) - "So when the sacred months have passed away, then slay the idolaters wherever you find them, and take them captives and besiege them and lie in wait for them in every ambush, then if they repent and keep up prayer and pay the poor-rate, leave their way free to them."  According to this verse, the best way of staying safe from Muslim violence is to convert to Islam.  Prayer (salat) and the poor tax (zakat) are among the religions Five Pillars.

Qur'an (9:14) - "Fight them, Allah will punish them by your hands and bring them to disgrace..."

Qur'an (9:20) - "Those who believe, and have left their homes and striven with their wealth and their lives in Allah's way are of much greater worth in Allah's sight. These are they who are triumphant."  The "striving" spoken of here is Jihad.

Qur'an (9:29) - "Fight those who believe not in Allah nor the Last Day, nor hold that forbidden which hath been forbidden by Allah and His Messenger, nor acknowledge the religion of Truth, (even if they are) of the People of the Book, until they pay the Jizya with willing submission, and feel themselves subdued."  "People of the Book" refers to Christians and Jews.  This was one of the final "revelations" from Allah and it set in motion the tenacious military expansion, in which Muhammad's companions managed to conquer two-thirds of the Christian world in just the next 100 years.  Islam is intended to dominate all other people and faiths.

Qur'an (9:30) - "And the Jews say: Ezra is the son of Allah; and the Christians say: The Messiah is the son of Allah; these are the words of their mouths; they imitate the saying of those who disbelieved before; may Allah destroy them; how they are turned away!"

Qur'an (9:38-39) - "O ye who believe! what is the matter with you, that, when ye are asked to go forth in the cause of Allah, ye cling heavily to the earth? Do ye prefer the life of this world to the Hereafter? But little is the comfort of this life, as compared with the Hereafter. Unless ye go forth, He will punish you with a grievous penalty, and put others in your place."  This is a warning to those who refuse to fight, that they will be punished with Hell.

Qur'an (9:41) - "Go forth, light-armed and heavy-armed, and strive with your wealth and your lives in the way of Allah! That is best for you if ye but knew."  See also the verse that follows (9:42) - "If there had been immediate gain (in sight), and the journey easy, they would (all) without doubt have followed thee, but the distance was long, (and weighed) on them"  This contradicts the myth that Muslims are to fight only in self-defense, since the wording implies that battle will be waged a long distance from home (in another country and on Christian soil, in this case, according to the historians).

Qur'an (9:73) - "O Prophet! strive hard against the unbelievers and the hypocrites and be unyielding to them; and their abode is hell, and evil is the destination."  Dehumanizing those who reject Islam, by reminding Muslims that they are merely firewood for Hell, makes it easier to justify slaughter.  It also explains why today's devout Muslims have little regard for those outside the faith.

Qur'an (9:88) - "But the Messenger, and those who believe with him, strive and fight with their wealth and their persons: for them are (all) good things: and it is they who will prosper."

Qur'an (9:111) - "Allah hath purchased of the believers their persons and their goods; for theirs (in return) is the garden (of Paradise): they fight in His cause, and slay and are slain: a promise binding on Him in truth, through the Law, the Gospel, and the Qur'an: and who is more faithful to his covenant than Allah? then rejoice in the bargain which ye have concluded: that is the achievement supreme."

Qur'an (9:123) - "O you who believe! fight those of the unbelievers who are near to you and let them find in you hardness."

Qur'an (21:44) - "We gave the good things of this life to these men and their fathers until the period grew long for them; See they not that We gradually reduce the land (in their control) from its outlying borders? Is it then they who will win?"

Qur'an (25:52) - "Therefore listen not to the Unbelievers, but strive against them with the utmost strenuousness, with the (Qur'an)."   "Strive against" is Jihad - obviously not in the personal context.  It's also significant to point out that this is a Meccan verse.

Qur'an (47:4) - "So when you meet in battle those who disbelieve, then smite the necks until when you have overcome them, then make (them) prisoners,"

Qur'an (47:35) - "Be not weary and faint-hearted, crying for peace, when ye should be uppermost (Shakir: "have the upper hand") for Allah is with you,"

Qur'an (48:17) - "There is no blame for the blind, nor is there blame for the lame, nor is there blame for the sick (that they go not forth to war). And whoso obeyeth Allah and His messenger, He will make him enter Gardens underneath which rivers flow; and whoso turneth back, him will He punish with a painful doom."  Contemporary apologists sometimes claim that Jihad means 'spiritual struggle.'  Is so, then why are the blind, lame and sick exempted?

Qur'an (48:29) - "Muhammad is the messenger of Allah. And those with him are hard (ruthless) against the disbelievers and merciful among themselves"  Islam is not about treating everyone equally.  There are two very distinct standards that are applied based on religious status.

Qur'an (61:4) - "Surely Allah loves those who fight in His way"  Religion of Peace, indeed!

Qur'an (61:10-12) - "O ye who believe! Shall I lead you to a bargain that will save you from a grievous Penalty?- That ye believe in Allah and His Messenger, and that ye strive (your utmost) in the Cause of Allah, with your property and your persons: That will be best for you, if ye but knew! He will forgive you your sins, and admit you to Gardens beneath which Rivers flow, and to beautiful mansions in Gardens of Eternity."  This verse was given in battle.  It uses the Arabic word, Jihad.

Qur'an (66:9) - "O Prophet! Strive against the disbelievers and the hypocrites, and be stern with them. Hell will be their home, a hapless journey's end."  The root word of "Jihad" is used again here.  The context is clearly holy war, and the scope of violence is broadened to include "hypocrites" - those who call themselves Muslims but do not act as such.

From the Hadith:

Bukhari (52:177) - Allah's Apostle said, "The Hour will not be established until you fight with the Jews, and the stone behind which a Jew will be hiding will say. "O Muslim! There is a Jew hiding behind me, so kill him."

Bukhari (52:256) - The Prophet... was asked whether it was permissible to attack the pagan warriors at night with the probability of exposing their women and children to danger. The Prophet replied, "They (i.e. women and children) are from them (i.e. pagans)."  In this command, Muhammad establishes that it is permissible to kill non-combatants in the process of killing a perceived enemy.  This provides justification for the many Islamic terror bombings.

Bukhari (52:220) - Allah's Apostle said... 'I have been made victorious with terror'

Abu Dawud (14:2526) - The Prophet (peace_be_upon_him) said: Three things are the roots of faith: to refrain from (killing) a person who utters, "There is no god but Allah" and not to declare him unbeliever whatever sin he commits, and not to excommunicate him from Islam for his any action; and jihad will be performed continuously since the day Allah sent me as a prophet until the day the last member of my community will fight with the Dajjal (Antichrist)

Abu Dawud (14:2527) - The Prophet said: Striving in the path of Allah (jihad) is incumbent on you along with every ruler, whether he is pious or impious

Muslim (1:33) - the Messenger of Allah said: I have been commanded to fight against people till they testify that there is no god but Allah, that Muhammad is the messenger of Allah

Bukhari (8:387) - Allah's Apostle said, "I have been ordered to fight the people till they say: 'None has the right to be worshipped but Allah

Muslim (1:149) - "Abu Dharr reported: I said: Messenger of Allah, which of the deeds is the best? He (the Holy Prophet) replied: Belief in Allah and Jihad in His cause..."

Muslim (20:4645) - "...He (the Messenger of Allah) did that and said: There is another act which elevates the position of a man in Paradise to a grade one hundred (higher), and the elevation between one grade and the other is equal to the height of the heaven from the earth. He (Abu Sa'id) said: What is that act? He replied: Jihad in the way of Allah! Jihad in the way of Allah!"

Muslim (20:4696) - "the Messenger of Allah (may peace be upon him) said: 'One who died but did not fight in the way of Allah nor did he express any desire (or determination) for Jihid died the death of a hypocrite.'"

Muslim (19:4321-4323) - Three separate hadith in which Muhammad shrugs over the news that innocent children were killed in a raid by his men against unbelievers.  His response: "They are of them (meaning the enemy)."

Tabari 7:97  The morning after the murder of Ashraf, the Prophet declared, "Kill any Jew who falls under your power."  Ashraf was a poet, killed by Muhammad's men because he insulted Islam.  Here, Muhammad widens the scope of his orders to kill.  An innocent Jewish businessman was then slain by his Muslim partner, merely for being non-Muslim.

Tabari 9:69  "Killing Unbelievers is a small matter to us"  The words of Muhammad, prophet of Islam.

Ibn Ishaq: 327 - “Allah said, ‘A prophet must slaughter before collecting captives. A slaughtered enemy is driven from the land. Muhammad, you craved the desires of this world, its goods and the ransom captives would bring. But Allah desires killing them to manifest the religion.’”

Ibn Ishaq: 990 - Lest anyone think that cutting off someone's head while screaming 'Allah Akbar!' is a modern custom, here is an account of that very practice under Muhammad, who seems to approve.

Ibn Ishaq: 992 - "Fight everyone in the way of Allah and kill those who disbelieve in Allah."  Muhammad's instructions to his men prior to a military raid.

Additional Notes:

Other than the fact that Muslims haven't killed every non-Muslim under their domain, there is very little else that they can point to as proof that theirs is a peaceful, tolerant religion.  Few verses in the Qur'an can be construed to fit the contemporary virtues of religious tolerance and universal brotherhood, and those that do are earlier "Meccan" verses that are obviously abrogated by later ones.  Small wonder that Muslim apologists spend a lot of time speaking of the "risks" of trying to interpret the Qur'an without their "assistance."

Far from being mere history or theological construct, the violent verses of the Qur'an have played a key role in the many massacres in Muslim history, including the brutal slaughter of tens of millions of Hindus for five centuries beginning around 1000 AD with Mahmud of Ghazni's bloody conquest, including the massacre of those who defending their temples from destruction.  Buddhism was very nearly wiped off the Indian subcontinent.  Judaism and Christianity met the same fate (albeit more slowly) in areas conquered by Muslim armies, including the Middle East, North Africa and parts of Europe, including today's Turkey.  Zoroastrianism, the ancient religion of a proud Persian people is despised by Muslims and barely survives in modern Iran.

So ingrained is violence in the religion that Islam has never really stopped being at war, either with other religions or with itself. 

Muhammad was a military leader, laying siege to towns, massacring the men, raping their women, enslaving their children, and taking what was once the property of others for his own.  On several occasions he rejected offers of surrender from the besieged inhabitants and killed those whom he could take prisoner.  He inspired his followers to battle even when they did not feel it was right to fight, threatening them with Hell if they did not, promising them slaves and booty if they did.  Muhammad allowed his men to rape traumatized women captured in battle.