By Clifford May

In one of his many magnificent books, Middle East scholar Bernard Lewis notes that in 641 C.E., the Caliph Umar "decreed that Jews and Christians should be removed from all but the southern and eastern fringes of Arabia, in fulfillment of an injunction of the Prophet uttered on his deathbed: 'Let there not be two religions in Arabia.'" I'm going to go out on a limb here and suggest that this had nothing to do with Jewish settlements in the West Bank or American support for Israel.

Fast-forward a few centuries: Today, many Muslims believe in peaceful and even cordial coexistence among Muslims, Christians and Jews. But such tolerant views are far from universal. In January, Dr. Imad Mustafa, a professor at Cairo's prestigious al-Azhar University, set out the justifications for jihad, or holy war. Among them: "To remove every religion but Islam from the Arabian peninsula." And, he said, jihad is also legitimate "to extend God's religion to people in cases where the government does not allow it"—in other words, to spread Islam and sharia, Islamic law.

Such rulings are not of merely theological interest. They lend legitimacy to violence directed at religious minorities. And indeed, in recent months, there has been a wave of attacks against Christians across what we have come to call the Muslim world. Churches have been bombed in Egypt, Iraq, Nigeria and the Philippines. In Indonesia, a mob of 1,000 Muslims burned two churches to the ground.

In Iran, scores of Christians have been arrested on various pretexts. In Afghanistan, a man has been jailed and is expected to be tried for converting to Christianity. Capital punishment is a real possibility. In Pakistan, a Christian woman was sentenced to death for the crime of making remarks that were regarded as insulting to Islam. The moderate governor of Punjab promised to pardon her and sharply criticized the blasphemy laws. But he was assassinated by a member of his own security detail, who afterward called his action "the punishment for a blasphemer." Hundreds of Pakistani Islamic clerics praised the killer's "courage" and religious zeal.

French president Nicolas Sarkozy has connected these dots and called the picture that emerges "religious cleansing." Pope Benedict XVI urged Christian communities in Muslim-majority lands to respond nonviolently to what he termed "a strategy of violence that has Christians as a target." The pontiff implored the governments of the Middle East to adopt "effective measures for the protection of religious minorities." The clerics at al-Azhar University called the pope's remarks "insulting" and suspended dialogue with the Vatican.

Most of the media have been ignoring this story or, in some cases, insisting that there is no story. If Christians are suffering in places where they are the minority, the root cause must be economics or politics or culture or misunderstanding—anything but intolerance and oppression based on Islamic religious doctrine. To believe this requires ignoring much evidence, not least the instances where, when a church is burned or a Christian murdered, the perpetrators yell, "Allahu Akbar!"

Investor's Business Daily recently quoted James Zogby, head of the American-Arab Anti-Discrimination Committee, offering a creative analysis. "The guy who gets up on the plane and says 'Allah!' or whatever and then blows the plane up is not making a statement about his faith," Zogby told congressional staffers. Zogby explained that it's like a Christian hitting his thumb with a hammer and exclaiming "Jesus Christ!"

"The comparison is absurd," IBD comments. "Muslims say 'Allah is greatest' to exalt their God. When Christians mutter 'Jesus Christ,' they are in contrast taking their Lord's name in vain."

Why should Jews care about Muslim persecution of Christians? Youssef M. Ibrahim, an Egyptian-born Coptic Christian and a fellow reporter back when we were both at The New York Times, puts it succinctly: "In the 1950s and '60s, they kicked the Jews out of the Middle East—everywhere but Israel, and, of course, they haven't given up there. Now, they are kicking out the Christians, too. It was inevitable."

What is not inevitable is the final outcome. Thirty years from now will the Muslim world—from Morocco to Indonesia—be "religiously cleansed"? Will other groups, for example the Kurds and Darfuris—Muslims but ethnic minorities—also be decimated or even exterminated? What about homosexuals—now facing severe persecution in Iran, Gaza and other places? What about women's rights?

Religious cleansing and the persecution of minorities in the Muslim world is not an easy problem to tackle. But surely the first step is to acknowledge that it is a problem—a major problem—and to begin talking about it candidly, understanding that some will complain they have been insulted or will level accusations of bigotry and "Islamophobia."

Long ago, there were Jewish communities in the heart of Arabia. They were exterminated by their neighbors, adherents to a dynamic, expansive and ambitious new religion. Not so long ago, there were Jewish communities throughout the broader Middle East. But in the second half of the last century, most Jews fled Muslim lands.

Today, there is Israel, a refuge for the Jewish people and an oasis of diversity and tolerance. If you think it's lonely and difficult for Israel now, consider what it will be like if all the nations surrounding Israel rid themselves of Christians and other minorities while the rest of the world—out of misplaced sensitivity or cowardice or some combination—averts its gaze.

Clifford D. May is a former New York Times foreign correspondent and the president of the Foundation for Defense of Democracies, a policy institute focusing on terrorism and Islamism.

This article was originally published in Moment Magazine.