The 7 July attacks in England last year once again drew attention to Pakistani madrassas, with allegations that a London suicide bomber had spent time in one.
The role of madrassas is viewed differently by East and West
The role of these Islamic schools has been an issue of concern for a long time - some are notorious for having recruited foot soldiers to radical Muslim movements.
After the 11 September bombings in New York, international pressure forced President Pervez Musharraf to try to bring madrassas under greater control.
Again, after the London bombings, he promised reforms.
Now officials claim most madrassas have registered with the government.
"They have to take an undertaking that there will be no teaching of sectarianism," says religious affairs minister Ejaz ul Haq, "no publication of any hate material, and no militancy."
The hardline madrassas teach intolerance of other beliefs, which sometimes leads to violence. Some observers are sceptical about just how effective the reforms really are.
"Actually what is significant is the types of madrassas that they want to target have just point blank refused to be registered," says Talat Aslam, Karachi editor of a newspaper called The News.
"The ones that are the most militant have just simply refused and the state has not been able to do much about it."
But those who run the madrassas say they have been unfairly targeted.
After all, there's still no proof that any of the London bombers attended Islamic schools here.
Still, after 7 July the government banned all new admissions of foreign students.
That hasn't gone over well at the Jamia Banooria Madrassah in Karachi.
The number of international students there has dropped dramatically.
Those who remain include 20-year-old Hena Haqe, from Chicago.
"Why is (President) Musharraf barging in and saying you can't do this?" she asks angrily.
"If he claims to be a Muslim then why is he trying to stop his own people from learning their own religion? It is totally wrong. Does (George) Bush do that? Does Tony Blair do that? It's so stupid, it's like saying leave your own religion and go back home."
Next door in a separate school the boys feel the same. They are a mixed group of friends, some want to be Islamic clerics, some were forced to come by their parents and just want to go home.
But all agree that 7/7 had nothing to do with madrassas.
"Madrassas don't teach people how to bomb places, they don't have sniper classes," says 15-year-old Saeed Hussain from Birmingham, England.
"We just stick to religion, we learn the Koran, that's it."
Saeed (back row, left) and Iftikhar (second left) feel stigmatised
They feel increasingly stigmatised for their choice of education. Fifteen-year-old Iftikhar Ilyas gets tired of being grilled by immigration officials when he goes back to Los Angeles.
"Sometimes some questions burn my heart, but sometimes I just laugh, because it's the same questions over and over again," he says.
"And some questions hurt, because you've been in Pakistan for so long, and nothing ever happened, so they ask these dumb questions, crazy questions in their mind."
For many here madrassas are not the problem. They say what drives Muslims to extremism is British and American foreign policy in places like Iraq, Afghanistan, and the Palestinian territories.
"Islam teaches one to refuse tyranny and to resist occupation, but students don't have to learn that in class," says Maulana Sami ul Haq, director of a leading madrassa.
"They learn that by following the news on TV and radio. The whole world is an open book about the double standards of the superpowers."
Pakistani madrassas are not all oases of Islamic study, some do promote sectarian hatred.
But neither are they factories producing international terrorists.
Mostly they are religious schools, whose role is viewed differently by East and West, as so much else is.