Mohammed Yusuf, leader of the Islamic sect whose members staged attacks across north Nigeria leaving 700 people dead last week, was facing charges that he had received money from an al-Qaeda linked organisation, defence analysts have revealed.
For years diplomats have feared a Nigerian al-Qaeda sleeper cell might launch attacks on the country's oil infrastructure, which is increasingly important to the US.
Nigeria, with its large number of impoverished, disenfranchised and devoutly Muslim young men, easy access to weapons and endemic corruption may seem to be the ideal breeding ground for anti-western radicals.
The presence of an al-Qaeda branch operating across the Sahara Desert in Mauritania, Morocco, Mali and Niger and Nigeria's porous borders have sharpened such fears.
But so far there has been no evidence of Osama Bin Laden's group in Nigeria, despite several arrests by the government and two warnings from the US about potential attacks on its interests in the country in as many years.
And analysts remain sceptical about any link between Nigerian radical Muslims and global jihadists.
The charges against Mr Yusuf were brought by the Nigerian government in 2006, but have never reached a court, says Will Hartley of Jane's Terrorism and Insurgency Centre.
Mr Yusuf was accused of receiving money from an alleged al-Qaeda group in Sudan to recruit young men to his organisation.
The money was given to him by Nigerian businessman Bello Damagum, who was also charged.
Mr Damagum said he did not want to comment on the allegations as the case is still pending, but the BBC understands the charges relate to money he gave to Islamic charities which send children abroad to learn the Koran.
It is common for wealthy Nigerians to make donations to Koranic schools in this way.
Nigeria has also claimed to have broken up an al-Qaeda cell - in 2007 the government arrested five men in three northern states.
But lawyers acting for the men said the only evidence was a few old weapons and quantities of fertiliser, common household items in the north.
The arrests coincided with the visit of then US deputy Secretary of State John Negroponte.
The men were held for several months then freed on bail, and their case has still not been heard in court.
Nigeria analysts say that although some Islamic sects in Nigeria, such as Mr Yusuf's Boko Haram, are prone to violence and have an anti-Western agenda, they have different goals to al-Qaeda, and are unlikely to turn into sleeper cells in the way western diplomats fear.
The name Boko Haram means Western education is a sin and the group wanted to overthrow Nigeria's government.
The group was also known as Taliban, although it is not believed the sect had any links to Afghanistan.
Such sects are too well known to hide in the communities where they live.
Adam Higazi a researcher on Nigeria at Oxford University says that, as in many places in the world, young Muslims might sympathise with Osama bin Laden's condemnation of the West but there is a long way from that to staging attacks.
"The rhetoric of Osama bin Laden may chime with some radical young Muslims in Nigeria, but that doesn't mean there is a financial relationship," he says.
Boko Haram launched simultaneous attacks on police stations in different parts of northern Nigeria - but their militants were mainly armed with machetes and hundreds were killed by the security forces.
Al-Qaeda tends to use more sophisticated weapons.
Nigerian Islamic sects are relatively parochial and inward-looking, concentrating on fighting the Nigerian government rather than a worldwide jihad, he says.
Furthermore, the Nigerian state has not collapsed to the same degree as in a country like Somalia where al-Qaeda has significant influence, says Professor John Peel of the School of Oriental and African Studies.
"Most Muslims I have worked with in Nigeria regard with horror any attempt to divide their community," he said.
Nigeria has a long history of Islamic uprisings against "corrupt" rulers, dating back to the largest in West Africa's history, the jihad of Usman Dan Fodio in 1804.
Dan Fodio unified the Hausa city states under what became known as the Sokoto Caliphate, and many subsequent sects refer to that time as a "golden age".
Nigerian Muslims who join revolutionary sects would argue that the time is again right for the replacement of a corrupt government with one inspired by pure Islam.
But the historical context means they have their own reference points and tend not to look abroad for jihadist inspiration.