The recent conviction of radical Indonesian cleric Abu Bakar Ba'asyir has brought the country's Muslim boarding schools, or pesantren, into the spotlight.
Ba'asyir's school in central Java is alleged to have taught many of the suspected perpetrators of last year's bombing in Bali.
A respected think tank, the International Crisis Group, says a small group of pesantren have been teaching a hardline message of jihad, or holy war, and they have become an easy recruiting ground for the extremist group Jemaah Islamiah (JI) which is widely believed to have been behind the Bali bombings.
JI seeks to establish a pan-Islamic state, and Indonesia, home to more Muslims than any other country on earth, appears to be central to its plans.
The fear is the schools are being used to groom a new generation of radicals.
It is hard to tell whether militant Islam is on the rise among young people in Indonesia. Most are preoccupied with finding a job or watching the latest movie release on DVD.
But Salahudin Wahid, a vice-chairman of Indonesia's largest moderate Muslim organisation, Nahdlatul Ulama, said that within some pesantren students are taught that they have an obligation to try to make the dream of an Islamic state come true.
"Some of them then come to think the ends justify the means, even violence. But they forget that Islam is a peaceful religion. It is very clearly stated in the Koran that we cannot kill people, not even ourselves," he said.
The headmaster of Darunnajah pesantren in Jakarta, Sofwan Manaf, is frustrated by the negative press that Islamic boarding schools are getting.
Around 3,000 students - boys and girls - attend his school, which has a high academic reputation.
"Yes we teach the Koran here from an early age, and we teach Islamic law and Arabic," he said, "but we teach our students about the different interpretations of Islam as well, so that they learn to respect different opinions," he said.
One of the students at Darunnajah, 17-year-old Umi, had some sympathy with the Bali bombers.
"They saw so much bad behaviour in Bali, with girls wearing hardly any clothes and things like that. They wanted to fix it but they chose the wrong way," she said.
Umi would like Indonesia to adopt Sharia law because she says its strict rules would allow everyone to live in peace. "There would be no more rape or killing," she said.
Her friend Restifan agreed. "If we live our lives the correct way we can be an example to others," she added.
But outside Darunnajah pesantren, not everyone was prepared to be patient.
One such person was Saleh Mahmud Nasution, a member of the youth wing of the Islamic Defenders Front (IDF), a hardline group which used to send gangs to smash up bars selling alcohol, but more recently encouraged volunteers to go to fight a jihad against American forces in Iraq.
Saleh is only 20 years old, but he is already a regular on the preaching circuit, espousing the message of direct action he has learned from his elders.
"Even the prophet Mohammed fought in more than 20 wars because he saw that there was no other way," he said.
Salahudin Wahid, a moderate Muslim leader, said radical groups may be attractive to young men because they offer a sense of purpose.
"First they feel there is great injustice in the world. They see the West dominating developing countries, and many of those developing countries are Muslim. So they get the idea that they are fighting a new kind of imperialism.
"It is partly a romantic notion, but some of these extremist groups also offer money and training to young people who see no other future for themselves," he said.
Saleh, of the Islamic Defenders Front, certainly believes himself to be on a mission.
He is studying Islamic politics at university and wants to dedicate his life to fighting for the introduction of Sharia law in Indonesia.
He said he respected people like the convicted Bali bomber, Amrozi. "Indonesia needs more people like Amrozi, people who are prepared to sacrifice themselves for their religion," he said.
Saleh said he would not want to carry out a bombing himself, but in all likelihood there are others who would be prepared to cross that line.
The challenge facing Indonesia's leaders, political and religious, is to prevent that happening.