In recent months, a spate of atheist books have argued that religion represents, as "End of Faith" author Sam Harris puts it, "the most potent source of human conflict, past and present."

Columnist Robert Kuttner gives the familiar litany. "The Crusades slaughtered millions in the name of Jesus. The Inquisition brought the torture and murder of millions more. After Martin Luther, Christians did bloody battle with other Christians for another three centuries."

In his bestseller "The God Delusion," Richard Dawkins contends that most of the world's recent conflicts – in the Middle East, in the Balkans, in Northern Ireland, in Kashmir, and in Sri Lanka – show the vitality of religion's murderous impulse.

The problem with this critique is that it exaggerates the crimes attributed to religion, while ignoring the greater crimes of secular fanaticism. The best example of religious persecution in America is the Salem witch trials. How many people were killed in those trials? Thousands? Hundreds? Actually, fewer than 25. Yet the event still haunts the liberal imagination.

It is strange to witness the passion with which some secular figures rail against the misdeeds of the Crusaders and Inquisitors more than 500 years ago. The number sentenced to death by the Spanish Inquisition appears to be about 10,000. Some historians contend that an additional 100,000 died in jail due to malnutrition or illness.

These figures are tragic, and of course population levels were much lower at the time. But even so, they are minuscule compared with the death tolls produced by the atheist despotisms of the 20th century. In the name of creating their version of a religion-free utopia, Adolf Hitler, Joseph Stalin, and Mao Zedong produced the kind of mass slaughter that no Inquisitor could possibly match. Collectively these atheist tyrants murdered more than 100 million people.

Moreover, many of the conflicts that are counted as "religious wars" were not fought over religion. They were mainly fought over rival claims to territory and power. Can the wars between England and France be called religious wars because the English were Protestants and the French were Catholics? Hardly.

The same is true today. The Israeli-Palestinian conflict is not, at its core, a religious one. It arises out of a dispute over self-determination and land. Hamas and the extreme orthodox parties in Israel may advance theological claims – "God gave us this land" and so forth – but the conflict would remain essentially the same even without these religious motives. Ethnic rivalry, not religion, is the source of the tension in Northern Ireland and the Balkans.

Blindly blaming religion for conflict

Yet today's atheists insist on making religion the culprit. Consider Mr. Harris's analysis of the conflict in Sri Lanka. "While the motivations of the Tamil Tigers are not explicitly religious," he informs us, "they are Hindus who undoubtedly believe many improbable things about the nature of life and death." In other words, while the Tigers see themselves as combatants in a secular political struggle, Harris detects a religious motive because these people happen to be Hindu and surely there must be some underlying religious craziness that explains their fanaticism.

Harris can go on forever in this vein. Seeking to exonerate secularism and atheism from the horrors perpetrated in their name, he argues that Stalinism and Maoism were in reality "little more than a political religion." As for Nazism, "while the hatred of Jews in Germany expressed itself in a predominantly secular way, it was a direct inheritance from medieval Christianity." Indeed, "The holocaust marked the culmination of ... two thousand years of Christian fulminating against the Jews."

One finds the same inanities in Mr. Dawkins's work. Don't be fooled by this rhetorical legerdemain. Dawkins and Harris cannot explain why, if Nazism was directly descended from medieval Christianity, medieval Christianity did not produce a Hitler. How can a self-proclaimed atheist ideology, advanced by Hitler as a repudiation of Christianity, be a "culmination" of 2,000 years of Christianity? Dawkins and Harris are employing a transparent sleight of hand that holds Christianity responsible for the crimes committed in its name, while exonerating secularism and atheism for the greater crimes committed in their name.

Religious fanatics have done things that are impossible to defend, and some of them, mostly in the Muslim world, are still performing horrors in the name of their creed. But if religion sometimes disposes people to self-righteousness and absolutism, it also provides a moral code that condemns the slaughter of innocents. In particular, the moral teachings of Jesus provide no support for – indeed they stand as a stern rebuke to – the historical injustices perpetrated in the name of Christianity.

Atheist hubris

The crimes of atheism have generally been perpetrated through a hubristic ideology that sees man, not God, as the creator of values. Using the latest techniques of science and technology, man seeks to displace God and create a secular utopia here on earth. Of course if some people – the Jews, the landowners, the unfit, or the handicapped – have to be eliminated in order to achieve this utopia, this is a price the atheist tyrants and their apologists have shown themselves quite willing to pay. Thus they confirm the truth of Fyodor Dostoyevsky's dictum, "If God is not, everything is permitted."

Whatever the motives for atheist bloodthirstiness, the indisputable fact is that all the religions of the world put together have in 2,000 years not managed to kill as many people as have been killed in the name of atheism in the past few decades.

It's time to abandon the mindlessly repeated mantra that religious belief has been the greatest source of human conflict and violence. Atheism, not religion, is the real force behind the mass murders of history.

• Dinesh D'Souza is the Rishwain Fellow at the Hoover Institution. His new book, "The Enemy at Home: The Cultural Left and Its Responsibility for 9/11," will be published in January.