Thursday, two teenage American boys finally arrived in Atlanta after being forced to spend four years in a radical Pakistani religious school that recruits for the Taliban.

Noor Elahi Khan and his younger brother Mahboob were tricked into traveling to Karachi by their Pakistani-American father, a taxi driver from Atlanta. He enrolled them in the Jamia Binoria, a school famed for its connection to the Taliban and other radical Pakistani jihadi groups.

For nearly four years the boys were taught rote memorization of the Quran and the narrow sectarian outlook of their school. Their case became known only when Pakistani-American filmmaker Imran Raza discovered them in 2005 while filming; he later undertook their rescue.

The story of the Khan brothers illustrates a little-known problem that is much bigger than these two boys. The brothers are “the tip of the iceberg,” says Erika Pertierra, who, with Raza, produced a documentary film about the boys called “Karachi Kids” (the scenes of the boys are moving, although the film is overwrought). Eighty other Americans are studying at Jamia Binoria, according to its headmaster. As many as 600 Americans may be studying in Pakistani madrassas (the term for religious schools), Pertierra says.

What will these students do, one must ask, when they return to the United States? Pakistani madrassas gained notoriety after Sept. 11 when the United States overthrew the Taliban in Afghanistan. Thousands of Pakistani and Afghan Taliban had been trained in Pakistani madrassas and learned little but scripture. I once visited one of the more infamous schools, Darul Uloom Haqqania on the main highway between Islamabad and Peshawar, where poor boys huddled over Qurans memorizing verses. They received free tuition and room and board and learned the virtues of jihad.

After Sept. 11, Pakistani President Pervez Musharraf pledged to modernize the curriculum of the schools. His project didn’t make much of a dent. One of the 2005 subway bombers in London, a Pakistani-Briton, briefly studied in a madrassa. When that became known, Musharraf pledged to deny foreign students visas, a pledge not kept.

The scope of the madrassa problem is smaller than some believe, but still very worrying. Only 1 percent to 3 percent of Pakistanis study in madrassas full time, according to data in Christine Fair’s benchmark 2008 study, “Madrassah Challenge: Militancy and Religious Education in Pakistan.”

Some terrorism experts, such as Peter Bergen, say involvement of madrassa graduates in the worst anti-Western terrorist attacks has been rare. The World Trade Center hijackers were mainly well-educated Saudis. Yet those figures don’t give reason to relax about Pakistani madrassas – or the Americans who study there.

Fair spoke to the Khan brothers while visiting Jamia Binoria in 2006. “It was clear that they were there against their will,” she told me. “I was appalled that no one was concerned.” The Binoria madrassa is “notorious,” Fair says, not because it actually trains militants, but because of its radical ideology – which even despises Muslims of different sects. Madrassas like Jamia Binoria, she says, “are places for recruiting.”

She fears that, as the numbers of suicide bombers increase in Afghanistan, recruitment may shift more to Pakistani madrassas. “We interviewed a number of failed suicide bombers (caught in Afghanistan) who had been recruited from madrassas” in Pakistan’s tribal areas, she says.

She also worries that some U.S. students in madrassas may become ripe targets for recruiters. “If you need someone who could get into the U.S. easily,” she says, holders of U.S. passports in Pakistani madrassas fit the bill.

How should U.S. officials address this problem? The answer is tricky: Parents can choose their children’s education, and the Khan boys’ father wanted it to be along traditional religious lines.

However, children can get religious education without a radical madrassa. Georgia law requires parents not to deprive their children of education. “Madrassa education should not make you unfit to return home,” says Fair. U.S. officials can certainly use this lever. They should be aware of how many U.S. students are attending madrassas, and the nature of those schools.

Meanwhile, Noor Elahi Khan has lost four years of high school and has few good options. Film producer Pertierra is seeking a way to get Noor the education he’s missed. She’s also started the South Asia Foundation for Education Reform to raise awareness about the need for reform of radical madrassas, and about the American boys there. You can learn more at www.safereform.org.